Simulation and Modeling

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3 How to generate an ecosystem model for wetland combined with some socio-economic output by which ecosystem functions and services can be determined?
By Kamrul Hasan · North South University

Kamrul Hasan · North South University

Thanks Macovsky and Leger.

Thanks Macovsky and Leger.

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3 Can you send me your documentations about ns2 (for instalation, simulation, all) please
By Nassima Bousba · Université de Béjaïa

Hemprasad Badgujar · Shri Guru Gobind Singhji Institute of Engineering and Technology

http://ceit.aut.ac.ir/~bakhshis/ns-2/NS-2.pdf How to Compile Ns2 on Windows Platform http://cs-study.blogspot.in/2012/12/ns2-installation-and-ubuntu.... [more]

http://ceit.aut.ac.ir/~bakhshis/ns-2/NS-2.pdf How to Compile Ns2 on Windows Platform http://cs-study.blogspot.in/2012/12/ns2-installation-and-ubuntu.html Installing Network Simulator in Linux (UBUNTU) http://kaushiksundar.blogspot.in/2012/08/installing-network-simulator-in-linux.html Introduction NS2 Network Simulator https://www.google.com/url? sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&ved=0CD8QFjAC&url=http%3A%2F%2Fkpath-routing-in-ns2.googlecode.com%2Ffiles%2FIntroduction%2520to%2520Network%2520Simulator%2520NS2.pdf&ei=lO32UN2LEcPJrAfgt4CADg&usg=AFQjCNHmptLjMtkTR3ieo9D0QHH2iFfiKg&sig2=fjWVfIr33dcM7jd4OZXDPw copy & paste above from https up to VfIr33dcM7jd4OZXDPw and paste it into browser

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6 Which tools do you recommend for visual presentation (animation) of process scheduling in an operating system course?
By Mohammad Al-Hakeem · Technische Universität Berlin

Edward Raider

VTK - Visual toolkit

VTK - Visual toolkit

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11 Gromacs Error: Too many lincs warning
By Nithin C. · IIT Kharagpur

Abhishek Tyagi · IFTM University

I think you may use follwing solution while performing gromacs, before starting gromacs paste this command and type enter then start your simulation, ... [more]

I think you may use follwing solution while performing gromacs, before starting gromacs paste this command and type enter then start your simulation, now you dont get LINCS error: export GMX_MAXCONSTRWARN=-1

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1 What is the best free software to model (3D) and simulate (dynamic) electro-magnetic motors etc.
By Peter Pohlmann

Francis Lajeunesse · University Laval

Hi, Some time ago I had to deal with finite element methods and I used FreeCAD to build 3D-models and Elmer to solve the equations. In my opinion I t... [more]

Hi, Some time ago I had to deal with finite element methods and I used FreeCAD to build 3D-models and Elmer to solve the equations. In my opinion I think FreeCAD is good and is very easy to use, but I guess it depends on the complexity of your model. I had some problems with Elmer for very detailed 3D structures, so again it depends of the complexity of the system to solve. You might want to use Gmsh or another mesh generator instead of using what is built-in Elmer. You can still start with FreeCAD and decide which solver to use afterwards. I don't have a great experience, but I hope this can help. FL

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2 Where can I find information about atmospheric turbulence modelling (especially dryden's and Von Karman's turbulence model)?
By Aman Verma · Indian Institute of Space Science and Technology

Robert Tardif · University of Washington Seattle

How about going directly to the source, with a document written by von Karman himself. Available from PNAS at: http://www.ncbi.nlm.nih.gov/pmc/articl... [more]

How about going directly to the source, with a document written by von Karman himself. Available from PNAS at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1079162/pdf/pnas01712-0042.pdf

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1 What is the relation between "critical exponent" , "fractal dimention" and "percolation threshold" in percolation?
By Elham Daadmehr · Shahid Beheshti University

Dimitri Petritis · Université de Rennes 1

Suppose that every edge of an infinitely denumerable graph $G$ is either occupied with probability $p$ or absent with probability $1-p$. Then define $... [more]

Suppose that every edge of an infinitely denumerable graph $G$ is either occupied with probability $p$ or absent with probability $1-p$. Then define $\theta(p)=P_p(0\leftrihtarrow \infty)$ where $P_p$ is the product probability on the graph and $0\leftrightarrow \infty$ means that there is an (infinite) path of occupied edges connecting 0 to infinity. The critical threshold is then defined as the value $p_c= \sup\{p\in[0,1]: \theta(p) =0\}$. Critical exponents are associated with different macroscopic quantities. For instance, consider the behaviour of $f(p)=E_P(|\{x\in G: 0 \leftrightarrow x\}$. Above the critical threshold, the previous expectation is obviously infinite. When $p\uparrow p_c$ the quantity $f(p)$ diverges as $|p_c-p|^{-\epsilon_f}$ where $\epsilon_f$ is the critical exponent of $f$. There are several other critical exponents, associated with other macroscopic quantities. As you realise from the definitions, there is no direct relationship between critical exponents and percolation threshold. As a very good introduction on all these topics, I suggest the excellent book of Geoffrey Grimmett, Percolation, Springer-Verlag

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2 What is the best mathematical model that describes the Tsunami?
By M. A. Helal · Cairo University

M. A. Helal · Cairo University

Thank you for your reply, but I think this answer need more free downloadable papers especially in applied Mathematics, or in Fluid Mechanics. Any wa... [more]

Thank you for your reply, but I think this answer need more free downloadable papers especially in applied Mathematics, or in Fluid Mechanics. Any way, I'm waiting more clear mathematical answers.

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Open Role of thiazole / thiopene ring in compounds showing activity against DENV targetting BOG pocket
It seems that molecules which show activity targeting the BOG pocket have thiazole (or thiopene) ring. At first I thought that the ring provides H - b... [more]

It seems that molecules which show activity targeting the BOG pocket have thiazole (or thiopene) ring. At first I thought that the ring provides H - bond interaction with AA residue in the cavity, but my docking result doesn't says so. Meanwhile, the aminoguanidine group shows H - bond interaction. Anyone can suggest the role of the ring?

By Heru Pratomo · University of Indonesia

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8 I have designed four monomers of the protein and I want to combine them all to form one molecule. How can I do that?
By Manoj Kumar · Acharya Nagarjuna University

Balachandran Manavalan · Korea Institute for Advanced Study

How about the size of the linker region connecting these monomer? You can go for protein-protein docking experiment. However, you need biochemical res... [more]

How about the size of the linker region connecting these monomer? You can go for protein-protein docking experiment. However, you need biochemical results to validate your complex.

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4 What is the differnece between NS2 and NS3?
By Nassima Bousba · Université de Béjaïa

Ahmed Hassan · African Institute for Mathematical Sciences

Regarding ns-2 Unicast: IP, MIP, DV, LS, IPinIP, SR. Multicast: SRM. MANET: AODV, DSR, DSDV, TORA, IMEP. Queuing: DiffServ, RED, WFQ, DropTail. R... [more]

Regarding ns-2 Unicast: IP, MIP, DV, LS, IPinIP, SR. Multicast: SRM. MANET: AODV, DSR, DSDV, TORA, IMEP. Queuing: DiffServ, RED, WFQ, DropTail. Regarding ns-3 Ipv4, IPv6, NAT, BGP, OSPF, RIP, IS-ISPIM-SM, IGMP/MLD and for MANET: OLSR.

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2 Simulation of a Generalized Hyperbolic random variable
By Francois Watier · Université du Québec à Montréal

Francois Watier · Université du Québec à Montréal

Greatly appreciated :)

Greatly appreciated :)

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34 Simulation in wireless sensor nets
By Nassima Bousba · Université de Béjaïa

Nassima Bousba · Université de Béjaïa

Ok

Ok

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3 Implemented Evolutionary Algorithms in C++
By Lars Freier

Jj Merelo · University of Granada

Did you try EO? It's an old library, but increasingly mature. http://eodev.sourceforge.net/ and has a very flexible model for implementing all kind of... [more]

Did you try EO? It's an old library, but increasingly mature. http://eodev.sourceforge.net/ and has a very flexible model for implementing all kind of stuff; all kind of things have also been implemented.

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13 Criteria for Energy Convergence in Molecular Dynamics?
By Carlos Bueno · Universidad Peruana Cayetano Heredia

Olujide Olubiyi · Forschungszentrum Jülich

I will quickly point out that what is often employed for convergence 'estimation' is the RMSD, and/or the potential energy neither of which is really ... [more]

I will quickly point out that what is often employed for convergence 'estimation' is the RMSD, and/or the potential energy neither of which is really very accurate in the real sense of it. However, one has to consider the particular requirement of the convergence since this will determine the acceptability of the convergence accuracy. What do I mean by this? If I am only interested in getting my system to an 'equilibrium' state with large forces from unphysical clashes removed in preparation for a production run, then RMSD (both of the coordinate and potential energy) is sufficiently accurate. On the other hand, if what I am interested in is the convergence of the trajectory, post-production run, then the measure of convergence must necessarily depend on the quantity of prime interest. Take for instance, in some studies I conducted sometime ago I had found it most relevant to employ the convergence of calculated chemical shift with respect to NMR chemical shift data in judging convergence. The important thing is to first decide the important quantity that best captures the aspect of the dynamics one is interested in, and to measure convergence based on that. One should also keep in mind that convergence is crucially dependent on the simulation length and sampling technique, especially when trying to obtain a perspective of the macroscopic state from the typically finite system simulated using MD.

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4 Numerical integration with forced input
By Fuyuki Hane · TOKYO KEIKI INC. Japan

Rami Maher · Isra University, Jordan

you should prepare a convolution integral considering the plant and the unknown input, then for every specific input, you can solve numerically using ... [more]

you should prepare a convolution integral considering the plant and the unknown input, then for every specific input, you can solve numerically using multiple Simpson's rule for finite time (usually from zero to steady 10 times the largest time constant of the system) with constant step of integration.

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2 Can anyone help me set up MCNPX on Windows?
By Rafael Medeiros · Universidade Estadual Paulista

Ali Alghamdi · University of Dammam

try mcnpx network, they have info about this topic

try mcnpx network, they have info about this topic

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4 Studies that compare the performance of strong form and weak form meshfree methods
By Renato Mesquita · Federal University of Minas Gerais

Renato Mesquita · Federal University of Minas Gerais

Hello Reza, Yes, my affirmation on the inefficiency of weak forms only applies to the meshfree context, not to FEM. I agree that parallel implementat... [more]

Hello Reza, Yes, my affirmation on the inefficiency of weak forms only applies to the meshfree context, not to FEM. I agree that parallel implementations would remedy the computational costs but this applies to all meshfree formulations, not only to those based on weak forms. I work with weak form meshfree formulations, but in my application area (Electromagnetism) people (especially those with a finite difference background) are using more and more meshfree strong form formulations. I wonder why this is happening and I think that a study that compares all the aspects of strong and weak meshfree formulations is something that must be done to clarify the issue. Best regards, Renato.

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6 How to model inventory replenishment policies and production strategies of a company?
By Zahrial Fakri · Universitas Syiah Kuala

David Lane · University of Reading

The entire field of System Dynamics Modelling was founded on an example of inventory modelling. There is a 1958 HBR article and the 1961 book 'Industr... [more]

The entire field of System Dynamics Modelling was founded on an example of inventory modelling. There is a 1958 HBR article and the 1961 book 'Industrial Dynamics' by J W Forrester. More information available from the System Dynamics Society:- http://www.systemdynamics.org/

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19 Probabilistic Modeling with DSMC/MC
By Dejan Petkow · European Space Agency

Dejan Petkow · European Space Agency

In the paper "Improved Direct Simulation Monte Carlo method for solving modern problems of rarefied gases dynamics" replace your references 20 and 25.

In the paper "Improved Direct Simulation Monte Carlo method for solving modern problems of rarefied gases dynamics" replace your references 20 and 25.

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4 What may have in common the elementary particles physics with hydrodynamics, differential geometry and our knowledge?
By Ovidiu Borchin · Carmit Chan Corporation

Gerard Baginski · Indian River State College

Elementary particle physics and hydrodynamics have absolutely nothing in common, unless you include a theory involving subatomic particles interacting... [more]

Elementary particle physics and hydrodynamics have absolutely nothing in common, unless you include a theory involving subatomic particles interacting in a macroscopic way in pipes. Let's be real, this is not real. Differential geometry has everything to do with everything. Our knowledge? Well, it is what it is and we are trying to increase it.

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4 Is anyone familiar with SimBiology (MatLab) and can you describe a functional conditional statement?
By Steph Hays · Harvard University

Mihir Arjunwadkar · National Centre For Radio Astrophysics - Tata Institute Of Fundamental Research

You are most welcome, Steph.

You are most welcome, Steph.

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12 What is the best way to estimate the condition number of a sparse matrix?
By Felipe Furlan · Universidade Federal de São Carlos

Shahid Amiri · Air University of Islamabad

it can be possibe only with the itrative method of LU and matlab

it can be possibe only with the itrative method of LU and matlab

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Open how can we make HiL test bench to be real-time?
if we connect a PC to a hardware by means of CAN protocol, how can we make it real-time?

if we connect a PC to a hardware by means of CAN protocol, how can we make it real-time?

By Mohammadjavad Esfandyari · University of Tehran

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7 MMPBSA calculation for a complex (containing 11 chain and 6 ligands)
By Pawan Gupta · National Institute of Pharmaceutical Education and Research

Alessandro Contini · University of Milan

Well, I don't know your system, so I can only give general suggestions. I would have run per-residue decomposition on a system were: complex=whole sys... [more]

Well, I don't know your system, so I can only give general suggestions. I would have run per-residue decomposition on a system were: complex=whole system (11 chains + 6 ligands) receptor = protein (11 chains) ligand = ligands (all six) Contribution of each ligand could be seen from the per-residue decomposition output (the .dat file that should have been produced) under the "DELTAS:" section. The other approach I mentioned before, can be pursued by performing six separate mmpbsa runs as follow: runX: complex=whole system; receptor=whole system "minus" ligandX; ligand: ligand X, where X correspond to each one of your six ligands (remember that topology files must be generated for each system). MMPBSA (or MMGBSA, as you prefer) might be directly obtained from the output. Hope to have centered your question,

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7 How to transfer Cartesian coordinates into Internal coordinates (bond-angle-torsion)?
By Jerry lee · Jilin University

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Question:
Open Source code of the protocol MMSPEED in MATLAB
Can anyone give me the code of MMSPEED with discrete simulation as I wish to see at least one flat multipath routing protocol in wireless sensor netwo... [more]

Can anyone give me the code of MMSPEED with discrete simulation as I wish to see at least one flat multipath routing protocol in wireless sensor networks?

By Nassima Bousba · Université de Béjaïa

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