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I am working on impact of a high speed metal particle on a substrate by FEA using Abaqus. The model is axisymmetric as shown in figure 1. I am using Coupled Euler- Lagrangian method for simulation. The substrate and particle is modeled as a Lagrangian body and the particle is placed in a Eulerian domain. I have created a discrete field for material assignment using volume fraction tool. The particle is then excluded from the simulation. The analysis procedure is Dynamics, temperature, explicit. The particle size is 25 microns. When I am using mesh size 1.5 microns for the particle, substrate and eulerian domain I am getting expected results as shown in animation1. But whenever I am changing the mesh size (increasing or decreasing) I am getting results as the particle is scattered or broken and impacting the substrate very randomly as shown in animation 2. Does anyone have ideas why this is happening?
The reference of the article I am using is
Xie, J., Nélias, D., Walter-Le Berre, H., Ogawa, K., and Ichikawa, Y. (October 1, 2015). "Simulation of the Cold Spray Particle Deposition Process." ASME. J. Tribol. October 2015; 137(4): 041101. https://doi.org/10.1115/1.4030257
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The volume fractions need to be updated after a mesh change. This is not associative.
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Hello dear researchers
I am working with a cubic structure and I want to substitute some atoms, but I have to take a 5×4×4 supercell. Will this affect the calculations, because my elementary cell is cubic and the supercell I just generated is not cubic? Are the results I had obtained correct?
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Hi Hamza,
Yes. Though it is a little better than that; the point of k-pt convergence is to determine how *dense* the grid of points needs to be; however when you make a supercell, the reciprocal space equivalent shrinks, meaning you will need fewer points to maintain the same density.
As a rule of thumb, if you double the supercell in a certain direction (adjust to your numbers as appropriate), then you will need half the number of k-points in that same direction.
Ideally one should converge on top of this, but it should give you a good place to start.
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I am New to MDS simulation which software will be open source and free tutorial available for beginners?
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Hi,
I have a little bit of MDS experience in 3 different software, so my opinion is based on these three:
1) Rich learning resources and analysis modules: Amber simulation engine
2) Beginner-friendly, good learning resources, and free: Gromacs
3) Pythonic and reasonable beginner-friendly but scarce analysis modules: OpenMM
In the case of Amber, the simulation engine is not free, while the rest of the resources are free, and its learning curve is steep. The various input files are difficult to understand in the beginning. However, Its analysis module contains almost everything. Plus, managing multiple trajectories/topologies during analysis is very easy.
Gromacs is easy to learn, however, the analysis module is not as rich compared to Amber. If you can somehow learn MDAnalysis (a python based MD analysis suite), then you can do almost everything required to analyze the trajectories.
For openMM, it is more suitable to develop and test new theories and force fields, however, you can run simulations using this.
There are other tools as well, like NAMD, CHARMm, etc but I don't have any experience in them, so I cannot comment.
Good luck.
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It's my first time using NAMD and I don't know how to continue my interrupted MD Simulation which was set up for 50 ns. I have my output.dcd and output.xst files and also log files.
Firstly I want to know how many steps have been completed? secondly, how to continue it to the total steps i.e 25000000 in the original namd file?
please provide the steps or command line needed during the restart of the simulation!
I really appreciate any help you can provide.
Regards,
Vinay
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Hi,
please check this, how to load.
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Manuscript is related to computational simulations of plant-microbe interactions.
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Why dont to find out a hybrid journal , publishing manuscripts both through open access as well as conventional publishing .
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I am using Abaqus UMAT subroutine to model wear damage between two contacting steel surfaces. I need to get the absolute maximum shear stress as it is a function of my wear damage model. I have tried using a utility routine called CALL SPRINC to get the 3 principal stresses ( σ 1,2,3). Since abs max shear stress = (σ1- σ 2)/2, ( σ 1- σ 3)/2, (σ 2- σ 3)/2 (the numerically largest of these).
However, it gives me principal stresses for each number of element and increment (which are thousands or maybe more than that), and I do not know how to assign the values to different variables in order to calculate the abs max shear stress using the eq. above. How do I assign the values in different variables?
I have also tried using the trigonometry (with the calculation of discriminant) to solve the cubic formulation to get the principal stresses manually but there is an error in trying to run the program as follow: The executable standard.exe aborted with system error code 1073741676.
1. Is there any way to directly get the abs max shear stress in UMAT subroutine?
2. How do I assign principal stress values in different variables?
Thank you!
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Which of the above two-mentioned softwares (i.e., COMSOL, or ANSYS Maxwell) are better in obtaining close results in the case of permanent magnets?
Also, what are the governing equations which are used in both these software? Are they same for both or different?
What are the boundary conditions, that are employed in each software for PM simulations?
Can anyone please guide me how we can proceed step-by-step, by employing governing equations and boundary conditions, etc.?
Any sort of calculations involved? Please help with that as well.
Thanx.
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Both software are good, but if you want to do a 2D simulation, I suggest you FEMM.
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Let's say we docked Protein X with Ligand A, Ligand B and Ligand C respectively.
Meanwhile, we have three different desktops, i.e. Desktops 1-3 for molecular dynamic (MD) simulation. Can we make use of the desktops using the following way in speed up the process of getting the results from MD simulation?
First round of MD simulation:
Desktop 1 - Protein X-Ligand 1 complex
Desktop 2 - Protein X-Ligand 2 complex
Desktop 3 - Protein X-Ligand 3 complex
Second round of MD simulation:
Desktop 1 - Protein X-Ligand 3 complex
Desktop 2 - Protein X-Ligand 1 complex
Desktop 3 - Protein X-Ligand 2 complex
Third round of MD simulation:
Desktop 1 - Protein X-Ligand 2 complex
Desktop 2 - Protein X-Ligand 3 complex
Desktop 3 - Protein X-Ligand 1 complex
Thank you.
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It is okay to do that. The results are supposed to be machine independent, so that peers can also reproduce the results. Make sure that the software version is the same in all three devices.
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Hello, I have attached an interval to alter the deposition of energy with time. How can we write this code using the expression language in FLUENT or CFX ?
Thank you very much !
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You can use a UDF file for older versions on Fluent (involve some quick C coding) or may just use the expressions box with some if condition statement (available in recent versions).
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Dear All: I am wondering if someone have an R codes (R functions) to run the test procedures described in the paper titled “ESTIMATION AND COMPARISON OF LOGNORMAL PARAMETERS IN THE PRESENCE OF CENSORED DATA” by STAVROS POULOUKAS 2004, Journal of Statistical Computation & Simulation, Vol. 74, No. 3, March 2004, pp. 157–169. I can send a copy of the paper if necessary. with many thanks abou
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Dear Researchers :
Recently I asked an official quotation (with all the requiered concepts) from ANSYS and from COMSOL to implement the same type of License and the same set of modules, the scheme of the License are not exactly the same , but very close ,
For both software I'm interested in being able to solve applications with the Structural Mechanics Module and the Electromagnetic Module
But in general, If I place both final prices in the same footage, I realise ANSYS is always more expensive (at least today) than COMSOL (roughly between 35 - 40 % more)
Does anyone with experience in this may know one of the reasons why this is so ?
Regards !
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Since I got more experience with scripting, I want to share my opinion from scripting point of view.
I found ANSYS more interesting than COMSOL because of its outstanding scripting capabilities. Depending on the module you want to use, ANSYS either uses JavaScript (e.g., DesignModeler and Mechanical) or IronPython (Workbench interface, Fluent etc.) in the background. In addition, Ansys provided APIs in IronPython programing language for almost all its modules (e.g., DesignModeler and Mechanical) which makes automation very easy. I mean you are not going to be limited to go with only one programming option and different gateways are provided for programing.
whereas, in COMSOL you will be limited to APIs provided in Java only, which is fine too.
This is my two cents and hope other people can share more great opinions from other perspectives.
Thanks,
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Hello.
I am running a molecular dynamic simulation of a peptide on the membrane for 1000ns. At the end of the simulation time my membrane looks weird, kind of wavy at the bottom bilayer membrane. I am not sure if this is normal or the problem that occurred during the simulation.
I have attached some figures . I really appreciate all opinion and explanation.
Thank you!
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Thank you
Nebojša Zec
!
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Hi Everyone, Hope you are doing well. I am trying to model the free standing mode of TENG in Comsol. As a beginner, I request you to please guide me if there is any free standing simulation model or tutorial video which I can follow to model this mode. I will be very grateful to you. Thank you
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Are you trying to find the fundamental mode?
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As a 2nd-year PhD researcher, I have been curious about the number of simulation-only PhD theses that exist in fields such as Engineering as well as unrelated fields as well. There is of course value in lab-testing, given how a simulation cannot always account for every boundary condition or factor. Usually, from my limited but growing experience, simulation, in the case of Additive Manufacturing and mechanical testing, is normally used as a validating tool; to help prove in a non-virtual environment what may be seen and tested in the lab, before any kind of scaling or future work is done using simulation (for cost-effectiveness and resource-saving etc.).
But in fields where in-situ testing is normally done, are there PhD theses that "Jump the gun" as it were, and go straight to simulation? Any information on this will be most appreciated given how, in some locations/countries where interaction and access to tools on campus and labs are minimal still due to Covid, improvisations must be made.
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Ezekiel Yorke I believe you partly answered your question in the last sentence of the first paragraph-"for cost-effectiveness and resource-saving".
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I am simulating cyclohexanone oxidation from a paper. I got the input files from supplementary data.
But when I am simulating, and generating Excel file at different temperatures the reactant Concentration is remaining the same and not decreasing neither the products composition is changing.
There is no reaction taking place. Please tell me how to resolve this.?
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Hi Shikhar, Could you solve the problem? I am facing a similar issue. Kindly suggest any method to resolve.
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I have a case, which is about internal flow with constant heat flux. Although the inlet boundary condition is laminar, the flow is passing transition and turbulent regime along the tube. As known, the intermittency term is 1 (so, admitted as turbulent inlet BC) for freestream velocity for external flow, I would like to learn that whether using the transitional SST model by laminar inlet boundary condition in the pipe is the corrects way or not.
Best regards,
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The problem I faced while using SST I need to put the value of turbulence intensity at the entrance, and if I specify it to zero then my solution does not converge.
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I want to learn theoretical research for energy applications. Please guide me for possible computational/simulation programming or software packages for research. Thank you.
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Hello Dr.
I think one of them is the Lumerical FDTD
or Comsol Multiphysics
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In experimental, the bond energy per atom rises quadratically with the number of bonds then why in simulations this bond energy per atom rises linearly with the number of bonds per atoms?
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I will get back to you soon.
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What is the proper course of action to be followed in solar cell device simulation?
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Dear Abhijeet Jaysingrao Kale ,
I am happy that you found my answer useful to you.
As for the optimization process, assuming that
z= f(x1,x2,x3,....xi,....xN)
with z is the function to be maximized, here it is the power conversion efficiency and the xis are the independent parameters.
To optimize this function you search for x1 to make z maximum keeping all other parameters constant and you repeat for all other parameters till you get the optimum values for all xis.
You may not get a peak value inside the chosen range of independent parameter xi. The chosen range of any parameter x is based on its realizability in the fabrication process.
The optimization process can be guided by the analytical solutions.
Therefore, the presence of the analytical solution is very useful and saves many computation efforts and gives physical insight.
I would like that you see the analytical solutions for the organic and pervoskite solar cells:
Till now there is an optimization method where one changes the all the parameters simultaneously to get their optimum value.
This solution may may take tremendous computational efforts without appreciable gian.
Since the fabrication process limits the possible values of independent parameter's. In addition as i said to you the analytical solutions give us an insight how we practically optimize the structure.
So, it is not a pure mathematical problem.
Best wishes
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I am trying to carry out the molecular dynamic simulation. Is there free software?
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GROMACS and NAMD/VMD are frequently used for molecular dynamics simulation of proteins
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I want to know that which is better in terms of graphics, modelling, dynamic simulation, and user friendly.
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Yes, just your email.
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I would like to know if it is possible to do MD calculations for protein on a regular PC? If it is possible, then what are some of the software that can be used and if there is anything i need to take in consideration before running the simulation.
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I'll just add some extra information to what Adron Ung said.
Keep in mind that to perform MD simulations you will need some minimum requirements. Although computing time is directly linked to the size of your system (e.g., protein size, water box, and etc), I'll say that based on my experience (I have performed simulation on all sort of PC and servers), you will need at least an 8 core, 16 GB computer, with a high storage HD, at least 1TB. Here is why.
Firstly, MD is not really based on RAM, they are linked to your processing power, thus, the more cores the better, and if you get it running on GPUs, it would be marvelous. However, RAM will always come in handy when dealing with other visualization programs, or some other software you might need to perform extra analysis. Second, depending on your system size, you will have massive outputs. For example, running a ~400aa protein in a dodecahedric box, using a united atom force field (like Gromos), for 50ns, only the trajectory final file might have around 20GB, and the .trr file (optional) will probably have around 80GB. After performing multiple simulations you will need a lot of HD space. If during the MD you run out of scape, your simulation will crash. You can perform the MD with fewer requirements if you want, or need, but it will demand your full attention on manipulating the outputs, saving them on external HDs, and having just being patient to wait for results.
Just some basic tips, if you have more questions I'll be happy to answer,
Cheers,
Bruno
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Hi,
I am trying to model Lamb waves propagation in an Aluminum plate using Abaqus. If I choose the frequency of 5-cycle Hanning excitation source is 0.2 MHz (to make sure that only 2 modes S0 and A0 appear in the result), the result showing good (see Fig.1) and the amplitudes of displacements does not decrease along measuring points (which have been proven by analytical approach). When I increase the frequency to 1.5 MHz (still have only 2 modes A0 and S0 depend on the dispersion curves in Fig.2) the results become disorder and instability, and the amplitude decrease along these measuring points.
Mesh size has been chosen to satisfy CFL conditions (= 1/15 x wavelength) and the time incrementation has been chosen to ensure that the fastest wave mode can propagate through element size (= element size / longitudinal wave speed).
So why the results become inaccurate?
Thank you for reading this post.
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Hi Ductho,
I believe that you have already tried an even finer mesh and the results are the same (convergence study). Maybe you should change the element type increasing the order of the shape functions (e.g. 2nd order elements if you use 1st order elements) because of the high frequency and wavenumber.
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Dear all,
I have experimental data for the effect of time at different feed concentration on the permeate flux of the hybrid adsorption membrane process for the removal of dye from wastewater. I would like to get a mathematical model.
I have a question please how to calculate the concentration at the adsorbent surface?
Would please help me to understand the calculation of concentration at the adsorbent surface?
I would appreciate your reply.
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What is there to explain? In the case of a batch process, m = (Co-C)V, where V = const. In a continuous (flow) process, V increases and C changes. Therefore m=∫(0->Vf) (Cin-C (V))dV, which definite integral can be calculated graphically as the area under the Cin-C vs V curve ( V = Fvt). Unless you mean describing the change in bulk concentration? Then the mass balance in the form of a partial differential equation/s.
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I am writing to inquire if there is a way to create a time-varying temperature field and apply it to a part on ABAQUS.
I am trying to model a cylindrical tank using the coupled temperature-displacement approach for thermomechanical stress analysis during the heating/cooling cycle (i.e., thermal ratcheting).
The model, solely composed of tank shell, will be heated up using a time-varying temp. field on the part’s surface. To this end I prepared the Spatial temp. data (X, Y, Z, Field value) at each time step “t”. But I am having trouble implementing this data on the ABAQUS platform. Could you advise on this matter?
FYI, the temperature data was calculated using the STAR-CCM program. In this regard, will my issue require the STAR-CCM-ABAQUS co-simulation process? I ask because I hope my issue is solvable just on ABAQUS with simple manipulations.
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I replicate the manual:
Defining time-dependent fields Abaqus/CAE Usage:   In Abaqus/CAE only predefined temperature fields are available. Load module: Create Predefined Field: Step: analysis_step: choose Other for the Category and Temperature for the Types for Selected Step: select region: Distribution: Direct specification or select an analytical field or a DISCRETE FIELD, Amplitude: amplitude_name.
Please note that DISCRETE FIELD (Distribution: (A) AnalyticalField; f(x): Type: Mapped field) can be inserted manually as tabular data (X,Y,Z,Temp) or read from file using context menu.
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Sometimes we hear somethings on stiffness problem of solution for chemical reaction modeling.
There is an option in Fluent software to figure it out.
Have you guys used it so far? tell us when and why did you use it?
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As Pierre Mandel kindly mentioned, when characteristic scales of your problem are very far (orders of magnitude) you see Stiff Differential Equations (ODE or PDE), It means you have small stability region or it means you have second or third order "Bifurcation" which needs a very high order numerical solution schemes and small time (discretization in general) steps.
There are two types of stiff problems in modeling advection-diffusion-reaction (ADR):
- If you model single specie, when time scale of Peclet number and Damkohler number are very different, you have an stiff ADE (or ADR, or transport equation), you can solve it either by implicit solver or small time steps, or dual time step, or other numerical tricks.
- If you have multi-rate mass transport and your species are internally related (reactive transport), you cannot solve this problem with small time step. Mathematically you have to get integral of infinity and you are always unstable. Those problem can only be solved with implicit solvers (all species in one shot!)
If you need more information on this topic, a very good and classic source for learning is this book chapter:
Approaches to modeling of reactive transport in porous media
Carl I Steefel, Kerry TB MacQuarrie Publication date: 1996/1/1 Reviews in Mineralogy and Geochemistry Volume 34 Issue 1 Pages 85-129 Publisher GeoScienceWorld
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Hello, everyone!
I've been trying to study the effects of some N-glycosylations in a sugar transporter. The in vivo experiments have already been performed, but I've been trying to add some N-glycans to this transporter in silico as well. I have successfully modelled some of the mutants, but there is a particular one that I've been struggling with. This mutant has 2 N-glycosylations in buried positions, and the in vivo experiments showed that these glycosylations greatly impair the transporter function. The problem is that I've been successfully adding the superficial carbohydrates, but I cannot add them in 2 buried sites. Could anyone help me with ideas on how these sugars could be added? Computer programs that can do that, or ways that I could unfold the protein, add the N-glycan and refold the protein would be extremely useful as well!
Thank you very much!
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If you are doing comparative studies to your other systems, totally unfolding the protein of one would likely result in uncontrolled errors in your study. What are you currently using for the superficial modifications? Are you doing all-atom simulations?
Something the may be able to help, which I've never used or tested: http://www.glycosciences.de/modeling/glyprot/php/main.php
However, what I would personally use is Chimera which has Modeller functionality with a GUI. Here is some background information on how it can be used for modifications: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-November/010526.html
You will need the model of the carbohydrate and then can build a bond/remove atoms. But, you will need a pocket to place it. You can drag regions of proteins in Pymol if needed and then perform energy minimization steps in Chimera of side chain rotamers and the added segments. You should be careful to not build an unphysical configuration though and check for clashes in Chimera, where there is also a built in function to quantitatively search.
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Guys, Sometimes after initializing the problem in Fluent and triggering the calculate button, a residual/residuals start from a big non-zero magnitude. For instance, to me, it in many cases happens for some convection-diffusion equation when I'm simulating combustion. Interesting point is that the results looks ok and have good agreement with experimental results. In this page:
It's said that:
"For most problems, the default convergence criterion in ANSYS FLUENT is sufficient. This criterion requires that the scaled residuals defined by Equation 26.13-4 or 26.13-9 decrease to 10-3 for all equations except the energy and P-1 equations, for which the criterion is 10-6."
As it is said, the residuals need DECREASE TO 10-3. Then it means that it doesn't matter from where the residual starts, it should finally decrease to 10-3.
  1. Am I right?
  2. What's your opinion?
Another question:
3. Why does it happans? (I mean why does the residual start from a non-zero magnitude?) and How to figure it out?
I've attached two screenshots of the residual of a project for instance.
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In my honest opinion there are many situations where this statement from the ANSYS Fluent manual is rather misleading, if not even wrong. In particular in CFD simulations with strong heat and mass transfer almost the entire physics, material parameters and thermodynamics is bound to a veery good convergence of the energy equation. In my opinion a scaled residual (RMS Res) of 10^-3 for the energy equation usually leads to rather physically wrong fluid temperatures (i.e. large errors in comparison to the real physics) with the corresponding consequences for the accuracy of the overall simulation.
The CFD best practice is:
1) define meaningful, local and sensitive physical target quantities (e.g. a temperature profile or a distribution of a certain sensitive species of your mixture).
2) run a series of CFD simulations on a reasonable resolved mesh (not the coarsest one) with systematically refined (and reached !!) convergence criterion, i.e. RMS Res<10^-3, <10^-4, <10^-5. And so forth, if still there is not yet a convergent trend.
3) Make a comparison of your sensitive target quantities from this series of investigations. If the target quantities do NOT change anymore significantly (in the range of your wanted error level of the simulation), than you have found your convergence criterion to which you need to converge own all of your following simulations.
Any other explanation or strategy is not leading to realiable CFD results i my opinion. You can read this strategy in the ERCOFTAC Best Practice Guidelines for Industrial CFD and in the ASME Standard for CFD Simulations and Heat Transfer. And once it is an European and American standard approach, I think we should strive to fulfill it, doesn't we as responsible engineers?
Best regards,
Dr. Th. Frank.
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I just started studying about computational chemistry. In particularly, I am interesting in calculating molecular properties by computational simulation.
Regarding to coupling constant between 2 atoms in a particular molecule, I have read some materials about DFT and Hartree-Fock approach. Both of them just use the coordinates (x, y, z) and charges of atoms as the input to calculate the properties. Did I understand it correctly?
Is there any other factors (e.g, hybridization, type of bonds,...) which affect to the calculation?
Could you please suggest any materials (papers or books) for this problem?
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I am planning to measure pressure and temperature variations in and around a metal vapour deposition chamber. The substrate is a steel strip, and I wanted to experimentally measure pressure and temperature variations, as you introduce the metal vapour in the chamber. I would aim to put these gauges in different locations of the vacuum chamber. I have been advised that because of the metallic vapour being introduced in the system, the gauge gets contaminated by the vapour and renders the gauges useless. Does anyone have any suggestions of pressure gauges that may work?
This is being undertaken as a form of validation for a computational simulation of a similar scenario.
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If you simply put your gauge head behind a screen in order to prevent it from being directly hit by metal vapour from the source you should be able to gain reasonable pressure readings.
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CHARMM and AMBER are the force fields used in the computational simulation for the properties of dna, protein, etc. I'd like to know that, when to use CHARMM or AMBER force field. Also is it necessary to do MD Simulation via both of them.
Thank You.
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The force field is an important "part" of molecular simulations. Its choice may affect the conclusions severely. Unlike @Ramir, I do think that it is perfectly valid to ask, why you chose a certain protein or not another one. The conclusions should always be checked, where they are force-field independent.
CHARMM and AMBER force fields differ in many aspects and also at various levels. For instance, the atomic charges were derived differently. The differences are not only in between the force field families, but also within them. For proteins, Amber03 is different than Amber12 or Amber99, and it is not straightforward to say, which one is the best.
Practically, I would recommend you to read articles which validate/compare force fields of your type of biomolecule and process of interest. You should, in ideal case, validate your choice of force field yourself on a set of experimental (or higher level theory calculations) data. Here I put a few references where to start:
folded proteins:
disordered proteins:
nucleic acids:
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Hello,
Molecular simulation can narrow down the search for the most promising structures by predicting and providing a detailed picture on the molecular scale.
Is there any paper have tested and proved experimentally the results that have been already predicted using molecular simulation for adsorption of gases in porous materials? "Not the other way around"
I'm looking for reference literature. Thanks in advance
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Hello!
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I want to simulate electromagnetic stirring of aluminium casting in which heat transfer and solidification of casting are observed. Is there any open source software simulating electromagnetic stirring of casting?
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I am simulating crystal structures of tricalcium silicate, dicalcium silicate, etc. to obtain the IR spectra of the molecules using CASTEP. When I do the Anaylsis of the IR spectrum, I can see all the vibrational modes. I want to understand the bending/stretching modes in the MIR/FIR frequency region - such as symmetric/asymmetric or in-plane/out-of-plane.
But, I don't want to confirm the type of modes only from vizualization, I want to quantify the type of modes, from the change in bond angle, amplitude of vector, direction etc. For this purpose, I want to know vectors for each atom of all the vibrational modes. I couldn't find this information in the CASTEP output file. I found a file .phonons file which was hidden but in that file, but the values are not matching with the IR frequencies and amplitudes as seen in the CASTEP output file or in the IR spectra window where I see the vibrational modes. I am not sure why they are different.
I would be obligded if I can get some help regarding this.
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Thank you Ratan for the information, I will through them.
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For a membrane  cell (made only by lipids) simulation what software is better?
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Roshan Shrestha, thank you very much!!
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I want to start studies in ideal MHD computational simulations. e.g. MHD instabilities in cylindrical Plasmas in a 2D approximation to start. Can anyone share with me some information (papers, books, websites and so on) to develope succesfully this activitie?
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I wish to generate some random numbers for simulation.I have an equation for rutherford scattering of electrons.I wish to simulate electrons at random angles for which i need different values of  cos(Theta).
How can i write a program and plot the graph of such a distribution where the theta takes random values from 0-180 and plots it against the energy?
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among tones of possibilities, the following simple command in MATLAB generates random numbers within a specific range (e.g., from a to b):
theta = (b-a).*rand(N,1) + a;
where, rand is a MATLAB function returning normalized values (between 0 and 1) drawn from a uniform distribution, a=0 and b=180 in your specific case, and N is the number of random values (N>=1).
you can finally plot your calculations using the plot function in MATLAB:
plot(theta,Ee)
hope this helps!
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Razavi
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Hi Vikram,
   If I understand your question, you want to be able to model a high frequency inductor in SPICE with the typical input file  (is this what you mean by "dot" model?).
If this is the case, you could model high frequency effects with an "equivalent" circuit model.   If the frequency effect is nonlinear (obtained from empirical data), you would need to write a C-code that fits the I-V characteristics over the entire frequency range. In this way, you would then include this into SPICE in the same way that CMOS models are included.
Regards,
David.
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Hi all,
Can any one please tell me how can I calculate the S parameters in cst when I use the plane wave?
Thanks
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Hi
I had the same problem but I used the way said here:
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I'm currently doing a set of simulations on penetration depth of ions in electronic devices, and I'm wondering whether or not the crystal structure of the materials in the backend (dielectrics, metallization) in a typical Silicon process has an effect on stopping power of these compounds. The most impact I'd expect for Silicon dioxide, which in the case of PVD and/or CVD deposition tends to be pretty amorphous, while a thermal oxide seems to be much closer to a crystalline form. Now the question is how much of a difference should I expect? My gut feeling is that for a deposited amorphous oxide layer, the density should be somewhat less than that of a perfect crystal. But is the difference large enough to actually make a difference in stopping power of the oxide?
I'm aware that stopping of ions in itself is somewhat of a stochastic process such that the resulting range of the ions is subject to a statistical distribution already on its own, therefore I wonder if it actually would make a noticeable change if the density of the oxide layer would lower by a few percent...
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Yes, generally there is a clear difference in density beween amorphous and SiO2 crystalline phases. Amorphous SiO2 (2.2 g/cm3), cristobalite cubic phase (2.33) and trydimite hexagonal (2.28)  are realtively close in densities but have lower density than alpha rhombohedral hydrothermal quartz phases (2.65 g/cm3).
In your case I believe the substrate is glassy silica, the CVD and PVD methods are supporting very similar densitites of deposited structures.
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Need to simulate coastal wave using ansys fluent on levee structure. As well as sediment. So, its gonna be three phase flow. I have been using VOF of fluid method but no success. 
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Dear Santosh,
In general, CFD packages have almost the same steps.
starting with geometry, meshing, initializing, specifying the boundary conditions, processing, and post processing.
It is suggested to start a simple model (with single phase, two phases, etc...). Move ahead steadily slowly, step by step. hereby, I have attached links you may counsel.
Regards!
Azd.
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Does anyone come across research paper in which flow past square cylinder is analysed for different angle of incidence and flow is in vertical direction?
Please tell me Research paper Title with author name.
Thanks in advance.
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Dear Chirag,
You can refer "Vortex-shedding suppression in two-dimensional mixed convective flows past circular and square cylinders" by Nadeem Hasan and Rashid Ali. Hope you may get some insights. Prof. N.Hasan has worked a lot on square cylinder. You can check his other publications also.
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Dear all,
I was trying poseview server for calculating 2D interaction of my compound with receptor. I recognize hydrophobic interaction and hydrogen bonds. In addition I also note another interaction depicted as a green line connecting two green dots. Please see attached figure. I am sure it is Pi stacking interaction. I just need to confirm it by you people... Please comment on it.. 
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Interaction between pi systems, indeed.
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I am doing a research for alternatives of animal-testing and I need to know the challenges for in-sillico model
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That the data thus generated is often considered artificial/synthetic and therefore not real. But one example that shows the potential power of simulation is when it points to, suggests possilities, that empirics/field studies has yet to highlight/will never highlight. As in the recent interests and conjectures related to Planet X-suggested by simulations. What is data is up for debate depending on which stage of enquiry you find yourself. Computer simulations are said to produce metadata that is based on a metamodel-this for many is a challenge.
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I really wish to know if there is any good and detailed practical material on L-System for plant growth and development apart from the Algorithmic beauty of plants?
I want to simulate the growth of waterleaf plant (Talinum triangulare) and see the effect of environment and other factors on the plant.
I have tried to use cpfg in L-Studio and I recently saw few articles on Blender, but all these seem not good for me to get the work done.
I will appreciate your comments and supports to find a solution to this task.
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I believe one of the best developed practical applications of L-systems is L-peach (see below). 
We have recently extended L-peach to be used with apples (Fiser, M., B. Shi, J. Ravi, P. Hirst and Benes, B. (2016). IMapple: a source-sink developmental model for Golden Delicious apple trees. in Acta Horticuluturae (InPress)). I will upload the reference when the paper is published. 
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I want to simulate multi-pass moving heat source using DFLUX. I understand that I should use for loop but couldn't get to work, so is there any example or similar case to it?
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can you post your current code?
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Cloud analyst simulator has three inbuilt load balancing strategies. If we want to add some new strategies, is this possible and how is it possible?
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In cloud Analyst you go to following options and add your code files there .
Go to Source Packages > cloudsim.ext.datacenter ,  where you can add your .java (dot java ) code files for different algorithms.
For Results you can review my paper attached here . 
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How to mesh a shell spherical crown area with only triangular plate element in ANSYS APDL?
Now I have one problem about a shell spherical crown, a part of a shell unit sphere cutted by z = a plane, eg:a=0.5, to be meshed with only triangular plate element in ANSYS APDL.
If anyone willing to guide me a step by step procedure to mesh this part of a shell sphere area problem with only triangular plate element in ANSYS APDL, it will be much appreciated.
Your response will be highly appreciated.
You can also post your reply or private
Thanking you in advance
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Dear Victor Moagar,
thanks for taking the time for my problem. The sphere crown area given is exactly what I imagine of. Thank you.
Best,
Yu
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I am planning to generate a microalgal specific growth rate as a function of environmental factors. The thing is that I have chosen the existing models and I only want to find the models constants for each single function. The question is for example, if I want to model the specific growth rate as a function of light intensity, how do I have to do the experiments? What I have in mind is as follows:
1-setting the light intensity on different values (e.g, 50,100,150,...)
2-starting the experiments with the same initial cell concentration and constant values of other factors
3- stopping the experiment the day after
4-calculating the specific growth rate for each light intensity
5-plotting the specific growth rate vs light intensity and finding the models constants
I have this problem with the time of the growth. Is 1 day enough or I have to continue or what? I don't have any idea about how long to continue the growth
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I do not like guessing, so the first point is making clear what your question is, i.e. what do you want to know:  to make clear my point: you might wish to measure growth rates of acclimated cultures, or you might want to know the effect of environmental changes on growth rate.
In the first case, you have to make sure that the acclimation process is complete (this might take a few generations (that is, a succession of several cell reproductions). In the second case, you have to run several growth curves with acclimated cells, get your mean growth rate and use these cultures to start new ones in the changed environment.
Once said this, you may avoid completely the lag phase, by using cultures which are still  growing exponentially or nearly so (you will get the hamng of this after running a few growth curves), and definitely you  will have to run experiments lasting a few days, to make sure of the point where your exponential growth ceases to be so.
here a couple of paper which might help to make clear my points
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I need to need to evaluate the field along a curve for a large number of curves in CST, for a large number of files and would like to create a macro that will automatically create the full results template required, but I can't find a way to do this.
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Robert, Please send me a sample file to do the macro for you.
Best regards
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Notice: A wall has been placed at portion(s) of an OUTLET boundary condition (at 13.3% of the faces, 1.3% of the area) to prevent fluid from flowing into the domain. The boundary condition name is: R1 Outlet. The fluid name is: Air Ideal Gas. If this situation persists, consider switching to an opening type boundary condition instead.
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A OUTLET condition in CFX means that only a outflow happens ALWAYS. But during solution, a pressure field next the outlet can be minor than the outlet prescribed pressure, and so doing, the fluid tends to return from outlet. As there is none information about a inflow stream, this condition will fail. To prevent this issue, CFX closes the faces in the regions where this is happening to prevent a inflow. This intends to avoid numerical instabilities.  A message will inform you about the % of the closed faces. These faces will have a free-slip condition for a while, till the inflow tendency is finished, and the closed faces will decrease in % till a outlet condition dominates all region. 
If the % increase, there are a strong tendency to inflow, or physically, this region has a re-circulation zone. And or will change the boundary condition, or extend your domain to a real outlet zone. It will depends on the case. 
The OPENING condition has some options. But all means - " both inflow and outflow can happens, the physics will decide" . In this case you will inform to the solver:
  • pressure ( as the outlet condition)
  • direction - fixed (normal) or free ( depends on the solution)
  • values of the other variables ( temperature, volumetric fraction, turbulent intensity, etc)
  • and some times the loss coefficient that emulates a pressure loss due a porous medium or other factor that causes a pressure drop. 
The entrainment velocity is calculated according to a Bernoulli's equation, including or not the loss coefficient in the relationship. It will part of the solution. 
There is other option, is in Expert Parameters tab. The solver can be set to ignore the backflow. But generally results in divergence. 
 Almost always this massage indicates that the boundary condition is not properly chosen, or the region is not in the better place. 
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Thanks.
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Zelimkhan is right; keep 0 or 90 degrees orientation and use angled wiring connections to build your circuit
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I can see a significant cytoprotection in the combination(1:10) drug doses than the individual doses (approx. >17%, MTT assay values). I now need to find the CI values and DRI values along with relevant plots for further study. Can compusyn assist me with the job?
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Of course, as any pharmacological effect, cytoprotection can be used with Compusyn software. You only have to stablish the right control for cytoprotection and use good desogn for measure the activity (chekerboard disign for example).
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This the deal , when I try to run siesta, e.g.:
mpirun -np 4 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out
appeared the mensage:
mpirun noticed that process rank 1 with PID 17811 on node guilherme-Inspiron-N5010 exited on signal 6 (Aborted).
And when I change -np 4 to -np 1 like:
mpirun -np 1 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out
it's ok... but this way it's a normal way... without parallel mode!!
Anyone know what is going on?!
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I had a similar problem, the compilation went fine, but the code ran in serial mode. Probably editing by hand the arch.make was the problem. To fix this, here is what I did:
cd ~/Siesta/siesta-3.2-pl-5/Obj/
sh ../Src/obj_setup.sh
../Src/configure --enable-mpi MPIFC=/home/cgoehry/Siesta/openmpi/bin/mpif90 FC=/home/cgoehry/Siesta/openmpi/bin/mpif90 --with-blas=/usr/lib/atlas-base/libcblas.a --with-lapack=/usr/lib/atlas-base/liblapack_atlas.a --with-scalapack=/home/cgoehry/Siesta/scalapack/lib/libscalapack.a --with-blacs=/home/cgoehry/Siesta/scalapack/lib/libscalapack.a
make
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If so, which tool can I use?
What tools are used for implementing cloud security concepts like encryption and digital signatures?
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To get the real feel of cloud, I suggest you to go for Open Source Private Cloud tools like OpenStack or CloudStack. When you get your implementation or experimentation done on real systems, then you will gain a lot of awareness and knowledge, which will embrace your further research findings. If you are interested in exploring more on Cloud Security, then you may find this paper useful: http://dl.acm.org/citation.cfm?id=2345474. You can also have a look at this research paper "eCloudIDS – Design Roadmap for the Architecture of Next-Generation Hybrid Two-Tier Expert Engine-Based IDS for Cloud Computing Environment" (Link: http://link.springer.com/chapter/10.1007%2F978-3-642-34135-9_36), which will explore you towards a cloud security architecture that was implemented on CloudSatck.
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Tools especially for trust evaluation based on the log details and feedbacks.
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My expertise is on WARMF, which is a simulation model for hydrology and water qualities of a river basin. I want to develop App of the model for cloud computing so that stakeholders can login, run the model and see the results. I know how to do it, but I have difficulty finding a business model for users to subscribe to the services.
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I am conducting thermodynamic research on TRNSYS modelling of thermal solar parabolic dish systems and wish to compare our model with existing TRNSYS or Matlab Simulink models for thermal parabolic dish components. There are limited models on STEC TESS libraries and I was hoping to get in contact with researchers  with Solar Thermal Parabolic Dish Component models (.m or .tmf model files). 
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I am conducting similar research on TRNSYS for concentrated solar power systems, in particularly absorption chillers. I am happy to help if you think it might benefit to your activities.
Kumar
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We would like to simulate the motion of a magnetic bead that is immersed in water and is subjected to an external magnetic field at the same time.
At the moment, we are trying to use COMSOL to simulate it.
Can anyone help me on what Physics module that I have to use?
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Dear Indra,
You can try to combine the magnetostatics and the particle tracing modules. But you can also try a different approach, by physically (geometrically) defining the bead and solving a 3-way coupled magnetostatics - CFD - moving mesh problem.
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Simulation computing of simple shapes.
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You could try COMSOL Multiphysics. What type of modelling exactly are you looking at ?
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Hello,
I am performing docking simulations with Vina. I chose 32 (max) torsion angles (that move largest number of atoms) on the ligand to be flexible. This results in very good binding pose and large affinities (~ -9.0 kcal/mol). However, when I see the ligand structure alone, its secondary structure is completely destroyed. The alpha-helix is unwound completely. 
Is this considered normal, that the ligand secondary structure completely vanishes after successful docking? Or am I doing something terribly wrong. 
Any help is appreciated.
Thanks
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May I suggest the following which is a follow-up of Vikash's remark... and a bit less drastic than freezing all torsion angles...
If you are using a pdbqt file for docking, your ligand file might start like this.
REMARK  9 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: C_1  and  C_11
REMARK       I    between atoms: C_1  and  N_3
REMARK    2  A    between atoms: N_3  and  C_4
REMARK    3  A    between atoms: C_13  and  C_14
REMARK    4  A    between atoms: C_16  and  C_17
REMARK    5  A    between atoms: C_17  and  O_19
REMARK    6  A    between atoms: O_19  and  C_20
REMARK    7  A    between atoms: C_20  and  C_21
REMARK    8  A    between atoms: C_29  and  C_32
REMARK    9  A    between atoms: C_32  and  N_33
--> The active and inactive torsions of your ligand are indicated.
What you could do is to mark the torsions defining the secondary structure of your peptide as inactive, and keep the other actives. This will prevent distortion of the secondary structure, while allowing flexibility of the side chains.
Once you gain a first estimate of your complex, you can then try to refine using energy minimization and/or molecular dynamics.
Nonetheless, Vikash's remark regarding the fact that Auotodock / Vina is rather optimized for smaller molecule remains. I'm not totally sure of what this will give. There should be other programs that are more adapted for peptide / protein docking.
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Kindly tell me which function or code would be used to stop the working of a water heating system, built in TRANSYS, for 3-4 months. The system will remain in working condition for the remaining months.
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Dear Aamir,
If you want to imitate case when system is off because of some abnormal situation (blackout, fault, human interruption etc.) I would recommend to do following. In TRNSYS 1-on & 0-off control function is used and controllers typically give 1 or 0 as an output signal. Create a txt external file with 0 for the off situation and 1 for all the rest simulation period. Link this file with TRNSYS and multiply values with output from controllers. This will give you normal operation with off period when you want.
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Any comments about its graphical interface, simulation and optimization resources, graphs, toolboxes, interfaces with other languages and applications?
What are the main limitations and difficulties in its use?
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Vensim is only useful for System Dynamics models, that is, models described by ordinary differential equations and algebraic state equations. It is not possible to model partial differential equations, or mixed-integer linear programs. Also, Vensim's capabilities for optimal control is rather limited (only local optimization of constant control is possible). If you can live with these restrictions, then you find in Vensim a user-friendly and efficient software, together with a lively community supporting it (the annual SD conference starts tomorrow in Delft, see conference.systemdynamics.org for more information).
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How can I create this file (if nobody can send it?)
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Hi, here is a simple method for you if you have linux and a xyz file.
If you dont have a xyz file, then you can find it very easily online for standard fullerenes.
Open the xyz file with your text editor. Change the C with B and N as appropriate.
Then open a terminal window and use open babel.
the command is: babel -i xyz input.xyz -o pdb output.pdb
if you have any problem you can ask again. and if you dont have linux I ll create it for you.
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Recently I've decided to change the output of my code from ASCII tab-separated files to binary ones, obviously for better performance.This code extracts EM field data in the form of 1D, 2D even 3D matrices, with an appropriate header referring to the variable name (e.g. Length(m) EM field value etc.). I would like to use a binary format for the same purpose, to store this kind of data (if possible in the same format) and import output files in popular statistical and data manipulation software. Searching around I found HDF, CDF and SDF file formats. HDF and CDF are more popular than the last one but I think difficult to use in such an easy problem like mine. Which one do you prefer or have you used before? Any kind of help is appreciated.
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My two cents: netCDF and/or HDF could benefit you a lot if you need to do visualization of your data as a lot of visualization software, whether open source or commercial, support these two formats.
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I simulated my sample but I just recognized that I input the data in degree unit. Or do I need to change into radian and run again?
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Its really helpful..i re run my simulation again...
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I would like to know if is possible to run FullProf in Parallel?
Because of the software Siesta, I already have the mpirun that I can run the siesta using 2 core only typing mpirun -np 2 siesta.
Is it possible to do the same in fullprof, such as:
mpirun -np 2 fp2k Sample?
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In order to use multiple processors the FullProf has to be compiled with special libraries like Open MPI. The process of parallelization is not always a trivial task. To my knowledge FullProf does not include multiprocessor capabilities. However you could try to split your refinement if you have e.g. multiple samples and run two or more processes at once. Linux then should balance the load between the two or more processors.
Possibly this will produce some "speed" gain.
Regards
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I have a protein-ligand complex. When I run the grompp program, I am encounter with this error: Ignoring obsolete mdp entry 'title'
What's this error about, and how I can solve it?
Another question: my topology file lacked a position restrained section, what do you think about this?
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Dear Javad,
Change SDMSO atomtype to SDmso in the ligand.itp file.
Best,
HHA
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If these values are validated with simulation in a simple geometry like tube flow, it would be helpful.
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Hello,
for a systematic search for suitable polymer solutions in water the following publications might be helpful for you.
Werner, F.; A. Mersmann: About the Rheology of Polymer Solutions Part 1: A Simple Method for Testing the Consistency of Data Sets for the Description of the Rheology of Polymer Solutions. Chem. Eng. Techol. 21 (1998) No.7, p.559-562
Werner, F.; A. Mersmann: About the Rheology of Polymer Solutions Part 2: A Model for the Prediction of the Concentration Dependence of the Rheological Parameters of Power-law Fluids. Chem. Eng. Techol. 21 (1998) No.8, p.644-647
With kind regards
Franz Werner
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There are various simulation methods available such as Monte Carlo etc. How to start with any material for simulation of its defects and impurities? How can we use simulation in synthesizing any material?
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Depends on what we are simulating. If it's effect of dopant on radioactivity in the solid state then we have to see its effect on the surrounding parent material atoms but if we're simulating its diffusion during solidification, then we have to get its transport properties and diffusion model during solidification. Maybe we can have more insight into the problem you're trying to solve.
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I would like to use GPU's to run micromagnetic simulations. What factors should I consider before buying one? Does anybody know of good source of info on the subject?
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Simulation work takes lots of computing, so in my view the first priority goes to Number of CUDA cores or processing cores, next the processing power of the GPU, that is in the GFLOPS (for single and double precision floating point numbers). GFLOPS is related to number of cores.
Next is the memory system (size and bandwidth).More memory means more capability of storing more data/info of the particles to be simulated, more memory bandwidth means faster transaction of the data between CPU-GPU or GPU-memory.
The Bus interface is also another factor. It determines the data flow rate between the CPU and GPU. If the data to be tranferred betweed the CPU and GPU is large, this factor should not be ignored. For example PCI-e bus.
Now talking about the cards available nowdays, the max CUDA core counts to be 2880 yielding 5300+ GFLOPS for singe precision and 1400+ GFLOPS for double precision calculations, 12GB GDDR5 memory giving 288 GB/s of theoretical bandwidth (as for Nvidia Tesla K40, and costs $5000+). On the other hand, Nvidia Geforce GTX TITAN Black Edition packs similar theoretical performance but at around $1200.
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Yes, it is sparse? In fact it is result of discretization of a PDE in a specific domain.
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Which potential is the best choice for considering the interaction between copper nanoparticles dispersed in water and which one is the best for interaction between water-copper nanoparticles?
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You can use tabulated potential or sutton chen potential ,.... For Cu-Cu interaction.
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