The focus of this group are the methods and tools for modeling and simulation.

• Oswald Osbourn

  Predicting impact of CGG repeats on 5'-UTR 2D and 3D structure

  I would like to computationally investigate the impact of different number of CGG repeats on 5'-UTR secondary and tertiary structure. I suppose that well known software like mfold would be enough forI would like to computationally investigate the impact of different number of CGG repeats on 5'-UTR secondary and tertiary structure. I suppose that well known software like mfold would be enough for predicting 2D structure but what (and how) to use for predicting the impact on 3D structure of RNA?
• Zahrial Fakri

  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 simulationI 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.

  Recent replies ⋅ Show All (4)

  • 
    Zahrial Fakri replied

    Damir Kalpic : thanks for the information you have entered My next project will learn that you send it later Alireza Tavakoli : Thank you very much I will learn this Germán Giraldo : I'm confusedDamir Kalpic : thanks for the information you have entered My next project will learn that you send it later Alireza Tavakoli : Thank you very much I will learn this Germán Giraldo : I'm confused by this comment sorry, maybe I am not too familiar with databases and also for the SAP of the DB is on the way i know i can do in linux, so true I could use these databases in a simulation in which part? if i could use it when running a simulation thank you very much for your help

    18 days ago
• Nutan Chauhan

  PC configuration

  Can anybody suggest me the best PC configuration used to run Molecular dynamics and docking in Schrodinger package?

  Recent replies ⋅ Show All (2)

  • 
    Tanima Shree replied

    I have worked with schrodinger. A simulation of 20 nano second will take around 10 days on a normal PC. Again, it depends on the size of protein & the no of timesteps.

    20 days ago
• Andres Morales

  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 (inI 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 Andres

  Recent replies ⋅ Show All (12)

  • 
    Jose Oteros replied

    I think the optimum number of clusters is a relative concept. I analyze graphically a dendrogram as result of a HIERARCHICAL CLUSTERING to determine the most appropriate number.

    22 days ago
• Robin Gras

  Follow the weekly report of a virtual evolving ecosystem’s very long run We study the evolutionary process and the emergence of species in a simulated ecosystem. We have conceived EcoSim, anFollow the weekly report of a virtual evolving ecosystem’s very long run We study the evolutionary process and the emergence of species in a simulated ecosystem. We have conceived EcoSim, an individual-based evolving predator-prey ecosystem simulation. The agents evaluate their environment (e.g., distance to predator/prey, distance to potential breeding partner, distance to food, energy level), its internal state (e.g., fear, hunger, curiosity) and chooses among several possible actions such as evasion, eating or breeding. The behavioral model of each individual is unique and is the outcome of the evolution process. This is the only simulation modeling the fact that individual behaviors affect evolution and speciation. We were able to predict species extinction using information about spatial distribution of the individuals, to correlated genetic diversity with the fitness of a species, to show that the overall behaviour of our simulation is deterministic chaotic with multifractal properties and to predict speciation events using some features describing the species properties. This approach will be also used to study the species abundance distribution, patterns and rates of speciation, the evolution of sexual and asexual populations, the interaction and diffusion of an invasive species or a disease in an existing ecosystem, etc. We propose a weekly presentation of a run of our simulation that will last for tenth of thousand of time steps at this site: http://sites.google.com/site/ecosimgroup/research/ecosystem-simulation/long-run. Every week we will add a page presenting a detailed summary of what happen in the system during the last 500 or 1000 time steps. We will show many graphs, videos and figures presenting the evolution of the system, including the number of individuals, the number of species, the amount of food available, the tree of life of the world, the distribution of age of the individuals, the evolved behavioral maps of some individuals, the variability of the gene alleles in the populations… This will allow following the ongoing evolutionary process and its effects on the whole world for thousand of generations.
• Bhavaniprasad Vipperla

  Is anyone working on Umbrella sampling in Gromacs?

  I would like to do umbrella sampling using Gromacs for my potein-ligand complex. Can anyone help me in this?
• manoj kumar Yadav

  Research scholar, BHU,Varanasi

  molecular dynamics simulation using Gromacs

  Recent replies ⋅ Show All (2)

  • 
    Bhavaniprasad Vipperla replied

    Dear Gloria Can we perform the simulations using gromacs for a protein complex obtained from molecular docking. presently i am doing simulations following the gromacs tutorial for protein-ligandDear Gloria Can we perform the simulations using gromacs for a protein complex obtained from molecular docking. presently i am doing simulations following the gromacs tutorial for protein-ligand complex tutorial in which iam using protein and ligand independently but not as a complex.

    28 days ago
• vijay shankar Kumawat

  Simulated Annealing

  For Implemenation in industries

  Recent replies ⋅ Show All (4)

  • 
    Hisham AL-Barmany replied

    More details about algorithm need to used

    Apr 26, 2012
• Umer Zahid

  Biomass torrefaction process in Aspen Plus

  Anyone having experience of Biomass torrefaction process in Aspen Plus? Help regarding torrefaction reactors will be appreciated.
• Lars Freier

  Better Algorithm than "fmincon" in Matlab ?

  I'm wondering if there is a better algorithm for parameter estimation than "fmincon" in Matlab. I got the question because for optimiztaion in linear programming it is recommended to use "cimplex"I'm wondering if there is a better algorithm for parameter estimation than "fmincon" in Matlab. I got the question because for optimiztaion in linear programming it is recommended to use "cimplex" or "gurobi" instead of the standard Matlab solver "linprog"

  Recent replies ⋅ Show All (14)

  • 
    Diana Santalova replied

    I would recommend Simulated Annealing algorithm, a realization can be found in R (function optim, method="SANN").

    Apr 19, 2012
• Pengcheng Li

  How to calculate shear modulus of polymer solution/network using Brownian dynamics?

  I have seen two different methods. One is clamping the end of polymer into the boundaries and shift one boundary relative to the other(so the simulation box is deformed). The shear stress isI have seen two different methods. One is clamping the end of polymer into the boundaries and shift one boundary relative to the other(so the simulation box is deformed). The shear stress is calculated by forces imposed on the boundary by the polymer, divided by the area. The other is using the Kramers-Kirkwood expression. Are they equivalent? Another question, how periodic boundary condition is applied to such deformed box in the direction parallel to the shear direction? If x is the shear direction, is it that if x<gamma*y, it adds L where L is the dimension of the 2D simulation box and its lower-left corner is located at the origin.
• Suraj Singh

  Can we model a fluid using any model other than continuum or discrete models already present?

  Can there be a model which would be different from what we already have which could ease the computational load in solving using present models?

  Recent replies ⋅ Show All (1)

  • 
    Bart Craenen replied

    Strange question, since a model can either be continuous or discrete. The classification is essentially binary. Where there is a hybrid model, one part of the overall model is continuously modelled,Strange question, since a model can either be continuous or discrete. The classification is essentially binary. Where there is a hybrid model, one part of the overall model is continuously modelled, the other discrete. If you know of a way of modelling fluids that is neither continuous or discrete, I'd sure like to know about it. So in the end I don't exclude the possibility, just that I find it very unlikely that there is one. Wrt computational load. This is usually dealt with through distribution or varying the degree of accuracy of the model.

    Apr 19, 2012
• Biplab Bhattacherjee

  QUERY

  Is there anyone working with MONTE CARLO SIMULATIONS??

  Recent replies ⋅ Show All (2)

  • 
    Bart Craenen replied

    That's a bit old hat isn't it?

    Apr 19, 2012
• Geoffrey Cadogan

  I am looking for MATLAB code for Brownian Bridge where the time interval is odd partitioned, i.e. not 2^n.

  I will consider any Brownian Bridge code written for MATLAB simulation.

  Recent replies ⋅ Show All (2)

  • 
    Geoffrey Cadogan replied

    Hi Mohammad: I haven't done any serious programming in years. Here's what I get when I try to run the code above from a directory other than the MATLAB defaultHi Mohammad: I haven't done any serious programming in years. Here's what I get when I try to run the code above from a directory other than the MATLAB default directory: ********************************************************************************************************************************************* ??? Error using ==> load Unable to read file PlotPaths.fig: No such file or directory. Error in ==> hgload at 43 fileVars = load(filename,'-mat'); Error in ==> openfig at 72 [fig, savedvisible] = hgload(filename, struct('Visible','off')); Error in ==> gui_mainfcn>local_openfig at 286 gui_hFigure = openfig(name, singleton, visible); Error in ==> gui_mainfcn at 159 gui_hFigure = local_openfig(gui_State.gui_Name, gui_SingletonOpt, gui_Visible); Error in ==> PlotPaths at 18 gui_mainfcn(gui_State, varargin{:});

    PlotPaths.m

    Apr 15, 2012
• Nutan Chauhan

  How to make a dimer of protein?

  I have a protein sequence whose str is to be predicted. This protein is a homodimer, what is the best way to model its dimer: 1. Shall I use Modeller software for homology modeling to make its dimerI have a protein sequence whose str is to be predicted. This protein is a homodimer, what is the best way to model its dimer: 1. Shall I use Modeller software for homology modeling to make its dimer directly based upon its template that as homodimer? If yes, shall I go for dynamic study of this dimer? OR 2. shall I go for homology modeling of one subunit using Modeller and then for docking by providing this homology model to make the dimer?

  Recent replies ⋅ Show All (7)

  • 
    Srinivas Penumutchu replied

    you can do homology modeling using known dimer ! i think no need of docking ! if you want do docking to define the residues .. you can use below linkyou can do homology modeling using known dimer ! i think no need of docking ! if you want do docking to define the residues .. you can use below link . http://haddock.chem.uu.nl/services/CPORT/cport.html

    Apr 14, 2012