Simulation and Modeling

Simulation and Modeling

  • Hasanthi anuradha Pathberiya added an answer:
    Does anybody knows a criteria to choose the optimal number of clusters in cluster analysis?
    I am trying to use cluster analysis to obtain conformations of a protein from molecular dynamic simulations data. But I have a problem to determine the optimal numer of cluster in the analysis (in this case conformations). Does anybody knows a criteria to choose the optimal number of clusters in cluster analysis? Any documetation about it?

    Thanks for your suggestions
    Hasanthi anuradha Pathberiya

    Try this

  • Komeil Hashemi added an answer:
    Any advice on explosion (detonation) simulation or modelling?
    I'm going to perform an explosion simulation. Any advice or suggested software?
    Komeil Hashemi

    In my opinion , LS Dyna is the best option. Has so many options and wide range of published work in different topics.

  • Richard Tran Mills added an answer:
    Any Free or Open Source Software (FOSS) for fluid flow simulation in porous media?
    The simulators I know are either not maintained, at a very early stage of development, or written in old programming languages, namely:

    * BOAST, UTCHEM, etc. written in Fortran 77 --
    * DuMuX written on top of a C++ library --

    If you know any alternative, please share.


    * MRST is a MATLAB® toolbox that is also part of the OPM initiative --

    * OPM is the best choice if you're a C++ programmer working in the field. Please invest time using it and contribute with code whenever possible --
    Richard Tran Mills

    PFLOTRAN ( is actively maintained and supported, written in modern Fortran 2003, has an extensive set of capabilities, and runs on machines ranging from laptops to the largest-scale supercomputers.

  • S. Mostapha Kalami Heris added an answer:
    Simulated Annealing
    For Implemenation in industries
    S. Mostapha Kalami Heris

    An open-source MATLAB implementation of SA, is available here:

    Also application of SA to VRP and Scheduling is available to download in the following links:

  • L. J. S. Sousa 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.
    L. J. S. Sousa

    Latex is my choice

  • S. Mostapha Kalami Heris added an answer:
    Fuzzy PSO Modeler
    Any body has a code to tune a fuzzy system using PSO in Matlab?
    S. Mostapha Kalami Heris

    An open-source implementation of tuning of parameters and training of a Fuzzy Inference System in MATLAB, is available to download, in the following link:

    In the provided source codes, Genetic Algorithm (GA) and Particle Swarm Optimization (PSO) is used to train a fuzzy system.

  • Mohamed Arar added an answer:
    Molecular dynamics in materials studio.
    When attempting to run a dynamics simulation using Discover module in Materials studio, I came across this problem:

    Error: Dynamics: Energy difference between successive steps in dynamics is greater than the user defined variable DEVIATION, 5000.000
    invoked from within
    "Dynamics \
    time = 5000.00 \
    timestep = 1fs.00 \
    initial_temperature = 298.00 \
    ensemble = NVT \
    temperature_control_method = ander ... "

    What could be the cause of this and how does one fix it?
    Mohamed Arar

    How many NPT simulations we have before we get the results

  • Ali A. Kazemi Afshar added an answer:
    How can I simulate storage zone inside intersection for left turns in Vistro or Synchro?

    In both program there are only way to simulate signalized intersection or roundabout.But in middle east, especially in Turkey or Iran there is some kind of signalized intersection, that exist a roundabout at the mid of intersection.So the cars are waiting in the middle of intersection instead of storage line.
    Just now, i want to simulate these kind of intersection in software in order to calculate level of service.

    Ali A. Kazemi Afshar

    I already try this method, but adding turn pocket storage increase the capacity of intersection so the delay of intersection decrease. Is there any alternative way without adding extra line as storage?!

  • Ravi Kant Avvari added an answer:
    Gromacs Error: Too many lincs warning
    I am trying to run an md simulation for 1ns for energy minimization of a pdb structure but everytime after 129 steps it fails with the error Too many Lincs Warning. What is the problem in simulation I dont know. Someone please help with this
    Ravi Kant Avvari

    Changing from md to steep help solved my LINCS + segmentation problem.


  • Monica Patrascu added an answer:
    Could it be possible implementing the fitness function of GA code in matlab to work with simulation rather than equations?

    I chose the GA for optimization by writing the program using ga code in matlab. This program is ok if I put the terms of fitness function as equations; for example:
    When I run the program the ga graphs and results is fine, and par=10.
    However, when I put these equations as a model in simulation, the ga graphs (best value) is constant (line) which is incorrect.
    My issue is that I need to import y1 from the simulation and y2 from data results to estimate par.
    Really I got stuck in this point which is how can I use ga with simulation.
    Moreover, I can share the knowledge with who is interested in.


    Monica Patrascu

    Oh, hello again. I forgot to check the questions, sorry, I don't get notifications. Here is an already implemented example of GA and simulink models:

    I hope it's not too late!

  • Fernando Agustín Otero added an answer:
    Is there a weaker condition rather than an isomorphism to keep properties from an original system to a mapped one?

    Let me explain myself. Suppose you have examined the structure of a typical integral system (might be just a discretised matrix version of it) and you have developed according to the properties of the system  some methodology. If you transform it (or map it) into another space, is it necessary for the other space to be an isomorphism or is there a weaker condition (or several) to assume all properties we found for the earlier case still apply? Just to make it clearer, I'm not talking of a weak formulation such as in the variational approach. Hope I could have explained myself. I can give a more detailed description of my concern if it is necessary.  I also would appreciate some articles or bibliography on this. Thank you in advance.

    Fernando Agustín Otero

    Thank you Dr. Apfelbaum. No, I don't actually want to go back to the initial space.

  • Arash Behnia added an answer:
    I need tutorial materials in modeling and simulation of wave propagation(Lamb,P,S and Ultrasonic) using ANSYS. Thanks in advance
    Modeling and simulation of Acoustics wave propagation
    Arash Behnia


    Why are not you using ABAQUS? You can also find a tutorial on youtube.

  • 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

    Maybe useful to you:

  • Georgi Genov 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.

    Georgi Genov

    Lets imagine the following situation - Little Johnny is a post-doc or a Ph.D. student; Little Johnny's boss/supervisor is active, with many collaborations and, therefore, appears as a co-author in hundreds of publications. Little Johnny happens to publish an article. His boss is, of course, the last co-author. Mind you, in many cases the name of the boss is there only out of courtesy. Some years later Little Johnny checks the number of self-references to his article, and finds a huge number of them. Little Johnny says to himself "How come? I've referred to this article just once in my entire life." Well Johnny, your boss has many new students. They write articles and refer to your research, but your boss's name is again in the authors list. And this counts as a self-reference for you.

    What do we do about that?

  • 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


    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

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

    Some of the articals

  • Christian Andersson Naesseth added an answer:
    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

    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

    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

  • Bernardo Alves Furtado 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.
    Bernardo Alves Furtado

    Hi there,

    I know of UrbanSim used by Paul Wadell to study metropolitan coupled systems of urban mobility and housing applied in Ohio and elsewhere.

    I also intend to fully develop this model for policy:


    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: This study simulates the evolution of artificial economies in order to understand the tax relevance of administrative boundaries in the quality of life of its citizens. The modeling involves the construction of a computational algorithm, which includes citizens, bounded into families; firms and governments; all of them interacting in markets for goods, labor and real estate. The real estate market allows families to move to dwellings with higher quality or lower price when the families capitalize property values. The goods market allows consumers to search on a flexible number of firms choosing by price and proximity. The labor market entails a matching process between firms (location and offered wage) and candidates (qualification). The government may be configured into one, four or seven distinct sub-national governments. The role of government is to collect taxes on the value added of firms in its territory and invest the taxes into higher levels of quality of life for residents. The model does not have a credit market. The results suggest that the configuration of administrative boundaries is relevant to the levels of quality of life arising from the reversal of taxes. The model with seven regions is more dynamic, with higher GDP values, but more unequal and heterogeneous across regions. The simulation with only one region is more homogeneously poor. The study seeks to contribute to a theoretical and methodological framework as well as to describe, operationalize and test computer models of public finance analysis, with explicitly spatial and dynamic emphasis. Several alternatives of expansion of the model for future research are described. Moreover, this study adds to the existing literature in the realm of simple microeconomic computational models, specifying structural relationships between local governments and firms, consumers and dwellings mediated by distance.
      Affiliation: Institute for Applied Economic Research (IPEA), CNPq, UnB
  • 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

    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

    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?
  • Muhammed Fasil 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)
    Muhammed Fasil

    Use a 1/z block or delay block just before that error showing block. 

  • Closed account 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


    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

    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

    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

    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

    Hi René,

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


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