Which software do you use for Molecular Dynamics simulation?

More Uttam Kumar Basak's questions See All

What does it signify that a system has strange attractors in phase space but its motion is not sensitive to initial conditions?

If I am not wrong, a dynamical system is called 'chaotic' if it satisfies the following two conditions: (i) having strange attractors in phase space, (ii) sensitivity to initial conditions. What...

10 November 2015 7,612 8 View

Can anybody suggest anything regarding parameterization of tetrachloroferrate (FeCl4-) ion?

I need the parameters for FeCl4- ion in any of the following force fields - GROMOS, AMBER, CHARMM or OPLS. The force field development of transition metal complexes is very difficult. I did a...

03 April 2015 5,680 7 View

Is there any model or equation for ridge dynamics?

I have a 2D system, you can think of it as a 2D sheet. There is a formation of ridges in this sheet when it is given a constant in-plane pressure. I want to model the ridge dynamics. Is there any...

06 July 2014 4,323 4 View

How can I calculate the interaction energy between two molecules as function of their separation?

I want to calculate interaction energy between two molecules as a function of their separation. I also want to see how geometry of the molecules affects their interaction energy. Can you suggest a...

04 May 2014 7,347 17 View

Is it possible to calculate the solubility of some material in water from the free energy of solvation?

I have obtained free energy of solvation in water using perturbation method with GROMACS. I want to calculate the solubility of the molecule in water. How can I do that?

31 December 2013 2,441 35 View

What if I define a dodecahedron box of a rectangular system of solvents? What will happen to the molecules outside the dodecahedron box during md?

I have solvated a ligand molecule with water molecules within a box defined by "inside box 0. 0. 0. 33.726 33.726 33.726" in packmol. Will it be meaningful and helpful to use editconf for defining...

09 October 2013 8,737 1 View

How to solvate a ligand molecule with a non-aqueous solvent like octanol?

I want to solvate a ligand molecule with (united-atom) octanol. I have a pre-equilibrated box of 512 (united-atom) octanol molecules. I am using editconf and genbox tool for solvating the ligand...

08 September 2013 8,632 8 View

Which one of the programming language do you think is better, Perl or Python?

I have used Python. It is simple and powerful. One of the crazy things about python is ipython shell. I don't know Perl. I have heard that it is an excellent scripting language. Which one do you...

08 September 2013 7,745 11 View

How can I get Antechamber working - it is giving an error message?

Antechamber from AmberTools13 is giving an error: " cannot run "..../sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit" " I have installed AmberTools13...

07 August 2013 4,873 8 View

Topology generated by ATB server contains a charge group of 32 atoms? Is it reasonable? How can I obtain the partial charges of atoms for molecule?

I have used ATB (http://compbio.chemistry.uq.edu.au/atb/) server to generate topology for piroxicam molecule (having 36 atoms). It has generated topology for GROMOS96 force field with two charge...

07 August 2013 6,707 7 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Mostafa Eidiani Popular answer

Please see: http://www.gromacs.org/Downloads

Supriya Das

Desmond

Mohammad Ali Mohammad

Materials Studio by Accelrys (http://accelrys.com/products/materials-studio/) -- Purchase of the relevant modules is neccessary though.

Dario Corrada

GROMACS, but I would like to use/learn/puchase AMBER... By the way, in our lab we have also Schrodinger's DESMOND module on local machines, but we don't know how to run it on a cluster machine with qsub tool. Any suggestions?

Justin Lemkul

GROMACS, NAMD, and CHARMM.

Marian Butu

Gromacs, charmm and vmd

Mostafa Eidiani

Mallikarjunachari G

Materials Studio is a good software for model building, and lammps is a good software for running simulations.