Simulation and Modeling

Simulation and Modeling

  • Stefano Papetti added an answer:
    What is the best TeX editor for LaTeX?
    Give your opinion especially on your experience whether good or bad on TeX editors like LEd, TeXMaker, TeXStudio, Notepad++, WinEdt (Paid), ....

    Some quick ref.
    Stefano Papetti · Zürcher Hochschule der Künste

    TeXmaker is my choice when I don't need a cloud based solution. I like it for its streamlined interface, including pdf rendering, doc structure, quick compilation with multiple pass for resolving bibtex references, all in one window. Unfortunately the latest version for Mac >10.9 seems to be bugged for dual screen use: drop down menus appear in the wrong place. It's a known issue due to the used Qt5 library.

  • Mehdi Rezaeianzadeh added an answer:
    Does a physically based nonpoint source model simulate mercury and nuclear waste?

    There are several hydrological and hydrodynamic models. I usually model nutrients transport using watershed models. Does a two-dimensional physically based nonpoint source model simulate mercury and nuclear waste?

    Mehdi Rezaeianzadeh · Auburn University

    Maybe useful to you:

  • Khaled Saad added an answer:
    Is self-citation good for showing the continuity of the research and avoiding self plagiarism? Please share your experience and thought.
    Self citation can help paper reviewers to check on the history of the author(s) and research topics.

    Any comment or opinion are welcome.

    Khaled Saad · Assiut University

    you can read this good article:

    Syed Wali Peeran, Aisha Mojtaba Ahmed, Marei Hamed Mugrabi, and Syed Ali Peeran. Simple steps to avoid plagiarism and improve scientific writing. Libyan J Med. 2013; 8: 10.3402/ljm.v8i0.21825.
    Published online 2013 Jul 25. doi: 10.3402/ljm.v8i0.21825
    PMCID: PMC3724953

  • Sima Abdi added an answer:
    Does anyone know any software to predict 3D structure of ssDNA aptamer (30mer oligonucleotide)?
    I am trying to study DNA (ligand)-Protein (receptor) Interaction by molecular docking, hence i need .pdb file format for DNA as ligand?.
    I would highly appreciate if you could please lend your valuable suggestions/advice to me.
    Sima Abdi · Islamic Azad University Tehran Medical Branch


    are ssdna that generaite in cell selex ir unstaible?

  • Tapan P Gondaliya added an answer:
    Scope of Digital Image Processing
    May i know what is the future prospective or the future scope after completion of PhD in Digital Image Processing?
    Tapan P Gondaliya · RK University

    may be this link and paper is useful to u..

    Some of the articals

  • Can someone suggest filtering methods for hidden Markov models with large state space?

    I was wondering if anyone has any good suggestions for solving the filtering problem when you have a hidden Markov model where the hidden chain x_k has a very large state space? By very large I mean that the exact solution ( becomes too computationally demanding.

    My application is basically a discrete spatio-temporal model where for each time instance the transition probability is a Markov random field with nearest neighbour interaction.

    Christian Andersson Naesseth · Linköping University

    Hi everyone, back from Easter break. Thanks for all the answers, I'll review them more carefully and make a more detailed answer later.

    To give some context to the problem I am trying to solve we have recently proposed a new particle filter/sequential Monte Carlo framework that does seem to work for quite a bit higher dimension than standard PFs. I have attached our arXived paper on the matter, the type of problems I am looking to find something to compare our method with is in Section 6.3. In this filtering problem we are looking at a structured state space where at each time step we would have to sum over 2^600 or 2^1056 different values using brute force.

  • Pranav D. S added an answer:
    I am looking for software for simulation of wind for Mac OS.
    I am looking for software for wind simulation for Mac OS. I use Ansys but I heard that there is no version for Mac. Is there any other software that you are satisfied with using? Is there a free version for students?
    Pranav D. S · Delft University of Technology

    For fluid dynamics, I'd suggest you try SU2 (Stanford University Unstructured) solver. The Euler and NS solvers are good. They use both direct and adjoint methods and it is possible to install from source on Mac OS

  • Randall Gray added an answer:
    Do you know any real example of use of agent-based models by decision-makers?
    These last years, I have developed many models to tackle real problems, but until now none of them have been used in real situations by decision-makers.

    I am curious to know if some of you have heard about examples of agent-based models that are actually used by decision-makers (city-planners, environmental health and safety manager, etc.) and not only by researchers/modelers.
    Randall Gray · CSIRO Marine And Atmospheric Research

    I've been involed in two large agent based magament strategy evaluation project designed to trial differeent wats of managaging the interactions between humans, human industry,  and ecosystems. I'll post some links to specific documents, but in the interim, you can look at papers on my profile, and the profiles of Beth Fulton and Rich Little.

  • Jafar Azamat added an answer:
    How namd and gromacs connection?
    CHARMM, X-PLOR, AMBER,and GROMACS are four types of force fields, and NAMD is ale to use all of them.
    so, I have a question how NAMD and GROMACS connection?
    Jafar Azamat · University of Tabriz

    There is no need to connect these softwares.

  • Amjad Ali Khan added an answer:
    Can anyone help with simulating WSN routing protocols?
    Does anybody know if the RMASE (Routing Modeling Application Simulation Environment) application for PROWLER simulator is still available anywhere for download? As far as I can tell there seems to be no official site or download links available anywhere.
    Amjad Ali Khan · National University of Science and Technology

    Sir did you manage to find the RMASE somewhere??? I also need it. 

  • Mahmoud Khaled added an answer:
    Mannasim patch file for ns2.35
    I have installed ns2.35 simulator to simulate a wireless sensor network routing protocol, but, they told me that I need a mannasim patch file to add, for correct working ns2.

    So please, if you can help me and tell me how to do that, if someone can give me the patch and how to add it?
  • Rasika Patki added an answer:
    Block Error Message
    Why do I get this Error message while I start the simulation, the error in the transfer function block: the message is:
    at time 0.0 is Inf or NaN. Stopping simulation. There
    may be a singularity in the solution. If not, try reducing the
    step size (either by reducing the fixed step size or by
    tightening the error tolerances)
    Rasika Patki · Walchand College of Engineering, Sangli

    Azzeddine Dekhane, i am facing the same problem as yours in my matlab simulation. did you find the solution for this error?? please let me know what is the solution if have found one.. thank you in advance

  • Simon Castro added an answer:
    Does anyone know how I can plot 3-dinemsional matrix with fourth attributes in MATLAB?

    Dear all
    I tried to visualize three-dimensional patterns in MATLAB using slice command and the plot attached in Figure 1_03012015.png which is not quite what I want.
    close all;
    obj = load('shadow.mat');% importing data
    dyzw = obj.dyzw;
    slice(dyzw, [], [], 1:size(dyzw,3));
    shading interp
    Instead, I want to get similar attached figure “Figure 2_03012015.jpg” but in color. This means I want to get rid of whole extent i.e. blue plate. Could you please help me in this regard?
    I appreciate your advice.
    Thanks in advance.

    Simon Castro · The University of Manchester

    Hi Mahesh,

    If you're talking about setting the alphamap parameters I'm not sure about this, as I haven't done this previously. Best to check the documentation (the link below has a worked example included for a surface plot - not the same but you should be in principle be able to do this for slice).

    If you wanted to set some pixels to NaN I would do the following. I'm not sure what format your dyzw array is in, but you can set anything above or below a certain threshold using the following lines of code:

    dyzw ( dyzw < thresholdLow) = NaN;

    dyzw ( dyzw > thresholdHigh) = NaN;

    This way, anything below thresholdLow and above thresholdHigh will be set to NaN and should appear as transparent. You will have to figure out appropriate values of these thresholds based on your data.

    Hope this helps


  • Akhilesh Akhade added an answer:
    How can I simulate an intrusion detection in an OPNET modeler?

    I need some information about how I can do an IDS algorithm in an opnet modeler simulation program. Can anyone help me?

    For Example: create a network contain an attacker, and victime and implementing our IDS approach

    Akhilesh Akhade · BITS Pilani, K K Birla Goa

    The link to source code is given below.

  • Edin Cerjaković added an answer:
    How to model inventory replenishment policies and production strategies of a company?
    I want to model the inventory replenishment policies and strategies in the production of a company by using a method to simulate, for example using a programming language to facilitate the simulation on a computer.
    Edin Cerjaković · University of Tuzla

    Hello Zahrial,
    good simulation tool for analyzing processes in to company (for the simulation process time from a few minutes to several years) is discrete event simulation.

    Your model can also be generated with discrete event simulation.

    I use Tecnomatix Plant Simulation (earlier: SIMPLE++ or eM-Plant), it is a very good tool with integrated programming language SimTalk, so that the most of non-standard problems also can be described.

  • Andrei Buin added an answer:
    How can I perform a simulation of a reaction using Gaussian?

    Dear All scholars,

    I want to simulate a 4 steps reaction over carbohydrates and anticancer drugs Gaussian, first of all, does the Gaussian have this ability to simulate this reaction and if so, i would appreciate anyone if he/she could give me some advises to do it?

    Andrei Buin · University of Toronto

    I'm doing something similar using CP2K. Basically one should look at enhanced sampling methods such as Replica Exchange Molecular dynamics. I have an implemenation of REMD on top of CP2K if needed i can send you. It is not going to work with Car- Parinello MD however should be fine with Born-Openhimer MD.

  • Jason M Swails added an answer:
    Suitability of amber force fields for high temperature MD simulations?

    Amber force fields generally used for low temperature simulation and results from amber force fields matches with the experimental data. So can we use amber force fields for high temperature simulations.  

    Jason M Swails · Rutgers, The State University of New Jersey

    I'll also add that the force fields were parametrized for room-temperature (or biological temperature) simulations.  I would not trust the validity of the force fields at much higher temperatures.

    With REMD, you actually don't have to care about this, because the high temperature replicas simply serve as a sampling reservoir that gets injected back into the thermally "relevant" simulations. This is done via a rigorous Monte Carlo criteria that ensures the overall ensemble will sample from the correct distribution, regardless of the "experimental correctness" of the higher temperature replicas.

    The most obvious place you can see the potential breakdown of the Amber force fields (and other, similar force fields by comparison), is the truncation of the valence potential energy term Taylor series (bonds and angles) to a simple quadratic function.  At low temperatures, bonds and angles may vibrate in a way that is mostly harmonic, so this is OK.  Go to higher temperatures, and anharmonicity becomes more important and so the functional form of the force field itself may begin to break down.

    This isn't to say that the force fields are for sure wrong at higher temperatures, but you would have to convince people they are right first.

  • Elena Gorokhova added an answer:
    Is anyone familiar with Iterations in STELLA models - how can I run them automatically?

    I need a suggestion from those who are familiar with STELLA or iThink (isee) modeling. How to run a model multiple times (>1000) and collect the output in a usable format?

    Elena Gorokhova · Stockholm University

    Hi René,

    Thank you, problem solved! I didn't realize that this is done via S-run. Thank you again.


  • Akhlaqur Rahman added an answer:
    Where can I get some resources for different types of Computation mathematical models and task graphs?

    For my research I need some technical knowledge about different types of a Computation mathematical models and task graphs. 

    Can someone suggest paper links or book names that may provide these info?

    Akhlaqur Rahman · Swinburne University of Technology

    Thank you for that. I think this will be great help. Appriciate this.



  • Shridhar Velhal added an answer:
    Is there any mathematical model possible for a suspension system which has 6-degree freedom?

    please suggest or share any idea regarding this.

    Shridhar Velhal · National Institute of Technology Calicut

    Mathematical model in given in following paper.  It may help you

  • Ehsan Mohseni added an answer:
    Has anybody used the MOVING MESH or DEFORMED MESH for a 3D model in COMSOL?

    Several times I tried to use these options to generate a movement for an eddy current simple circular coil (solenoid) in comsol and every time I failed to proceed.

    I was supposed to apply the moving mesh or deformed mesh to simulate the movement of coil on a fixed conductor (simple scan) in time domain (time dependent simulation) and also at same time measure the variations of coil inductance due to its movement on the conductor (a stationary frequency domain simulation), I have my models in hand, in case anyone feels like to help me on that , I will be more than happy to send my models for your comments.

    Best Regards,


    Ehsan Mohseni · École de Technologie Supérieure

    Hi Hossein,

    Thank you for the response. Being honest I don't have the version 4.3. the oldest version that I have here is 4.4 but I'll try to download the one that be compatible with you version in coming days. Thanks for your interest to help. I'll get back to you soon.



  • Closed account added an answer:
    Can any one help in the parameterization of ZN metal using MCPB?

    I want parameterise the ZN metal, which is coordinated with CCCH (three CYS and one HIS residues) residues. I just followed MCPB tutorial. While side chain modelling i got errors and unable to fix the problem. Here, i have attached my pdb file , sidechain.bcl file and sidechain.bcl log files.

    ANDDEAR RESEARCHER,I AM THE FIRST ONE TO ANSWER,HERE IS MY COMMENTS, the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.
    PMID: 20856692 [PubMed] PMCID: PMC2941202 Free PMC Article
    Share on FacebookShare on Twitter

  • Jean-Michel Bergheau added an answer:
    Which simulation tool can be used to simulate diffusion of nitrogen into the metal during nitriding?
    Jean-Michel Bergheau · École nationale d'ingénieurs de Saint-Étienne

    You can check the capabilities of the Finite Element software SYSWELD. I think you could be interested with the following papers :

    J M Bergheau, J Devaux, P Duranton, R Fortunier, M Larreur, J B Leblond, « Numerical simulation of superficial diffusion and precipitation of chemical elements, with application to some nitriding process », Surface Treatment VI, edited by C.A. Brebbia, J.T.M. de Hosson, S.I. Nishida, ISBN 1-85312-962-3, 2003, pp. 297-306.

    E. Feulvarch, J.M. Bergheau, J.B. Leblond, « An implicit finite element algorithm for the simulation of diffusion with phase changes in solids”, International Journal for Numerical Methods in Engineering, n° 78, 2009, pp. 1492-1512.

  • Paul Krot added an answer:
    Multiscale modeling of steel microstructure
    My questions for discussion are as following.

    1) There are a lot of publications on multiscale modeling of steel microstructure using standard FEM, special FEM, molecular dynamics methods (discrete elements, moving cellular automata) with quite nice images of simulations. How to varify results of simulations in grains boundary deformations and strains, grains growth and fragmentation as we will never have exactly the same pictures under microscope, moreover 2D instead of 3D. What criteria of microstructure models correctness? I think only statistical parameters of grains distribution (before and after deformation) can help in validation. Is any other opinions?

    2) There are several methods to produce ultra-fine grained (UFG) metals (ferrous and non-ferrous) with grains less than 1 micron by the severe plastic deformation (SPD) (ECAE(P), HPT, ARB, asymm. rolling-AR). Is anybody here who has a deal with steel microstructure multiscale simulation in SPD processes?
    Paul Krot · National Academy of Sciences of Ukraine, Z. I. Nekrasov Iron and Steel Institute

    Thanks, Pardis. Happy New year

  • Scott Lett added an answer:
    Does the Smith, Hucka et al method for hierarchical model composition uses many features of previous modeling methods?

    In 2003, in U.S. Patent Application 20030009099, Lett et al disclosed a component-based design pattern that facilitates hierarchical model building and model sharing.   In 2009, the Randhawa, Shaffer & Tyson article in Bioinformatics used a very similar approach.  While the authors acknowledged that some commercial applications implemented hierarchical composition of model components, they did not know of the public disclosure in application 20030009099.   I'm curious if the authors of Smith, Hucka, Hoops et al might comment on similarities and differences between the approaches?

     Randhawa R, Shaffer CA, Tyson JJ. Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinformatics 2009;25(24):3289-3295. doi:10.1093/bioinformatics/btp581.  

    Thank you, Tarik.  
    I am a big fan of the COMBINE effort, and proud to have collaborated with many pioneers in this field for over a decade.   It is gratifying to see so much momentum.  While I am not active in this area now, I retain an intellectual interest, and hope to keep up with what's new, and selfishly curious if  any of our contributions were of lasting value.  Wishing continued success,

  • Yuemin Hou added an answer:
    Are there methods (and tools) that can be used equally well for modeling the architecture/operations of HW, SW and CW constituents of complex systems?

    Integral and uniform modeling of hardware (both analog and digital), software (both system and application), and cyberware (knowledge structures, ontology contents, and data structures) of complex systems in the pre-embodiment and embodiment phases of development seems to be a challenge. Finding methods and tools, which cover each of the three domains, is difficult in the literature. Please advise if any trans-disciplinary method exist for architectural and operational, or possibly for a hybrid modeling, of complex systems.

    Yuemin Hou · Tsinghua University

    The key is to model behaviours.

  • Closed account added an answer:
    Using Real Time simulation in the case of off-line simulations has no problem to solve equations, could be an advantage to enrich research or no? Why?

    I have applied a new application on excitation of a generator. The simulation is carried out on Matlab environment. But the question is: regarding to the application is applied within excitation system ( it means the applied controller is local and destination factor is not a concern.) using Real Time simulation could be an advantage to enrich research or no?

    Thanks for your useful comments

  • Rick Vleugels added an answer:
    Does anyone know about a computational method to calculate if a molecule would form H-aggregates of J-aggregates?

    I have done some measurements on a small, rod-like, rigid molecule and I'm thinking the molecule switches over time from h-aggregates to j-aggregates. I was wondering if there are some computational methods to confirm this?

    Rick Vleugels · University of Leuven

    Thank you! The article looks very interesting. I'll look into it.

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