Dr. Rohan Meshram

9 Questions 34 Answers 0 Followers

Questions related from Dr. Rohan Meshram

What is the exact difference between restart files and restart.old files generated as output during NAMD simulations?

When one Performs MD simulations using NAMD. It generates restart files coordinates (.coor), velocity (.vel) and xsc (.xsc) files. It also generates restart files with extension .old. My question...

09 September 2019 7,191 3 View

Any idea regarding alpha and beta values in LIE molecular dynamics simulation of MHC-Epitope complex?

Hi, We are trying to perform MD simulation of MHC-Epitope complex and infer free energy following Linear Interaction Energy method. I know that the van der Waals and Electrostatic terms of bound...

10 October 2015 5,420 0 View

How can I keep my protein inside a water-box throughout simulation using NAMD?

I am trying to run a production run of 1 nano second in NAMD. Everything is OK till first few hundred Picoseconds. But after that my protein runs out of water-box. please have a look at frames of...

12 December 2014 1,890 5 View

Regarding amino acid nomenclature, are there are software or codes that revert alternative names of Histidine (HSE/HID) to normal HIS?

I have a molecular dynamics trajectory and I wish to perform further study on the last frame. While generating PSF and during course of MD simulation, NAMD and VMD changes 3 letter code of...

11 November 2014 4,084 5 View

Any idea about good online tutorial for doing Steered molecular Dynamics simulation using Constant Force Pulling method using NAMD?

Dear all I have DNA-ligand as well as protein-ligand system and I wish to do Steered molecular Dynamics simulation using Constant Force Pulling method using NAMD. I just need to know if you guys...

09 September 2014 2,630 2 View

Need help in relating time scale of MD simulation with 'numstep' and 'timestep' values using NAMD

I wish to know the simple relationship between 'numstep' and simulation time. I mean, if I wish to run a one nanosecond simulation what should be the value that I should put in front of the...

06 June 2014 5,812 4 View

Can anyone help with python scripts to analyze AutoDock results?

I am using PyRx interface for running AutoDock 4.2 After docking I get .dlg files as usual. now i wish to create complexes of poses obtained from dlg file. There are these two python scripts to...

05 May 2014 5,499 2 View

Problem running 64 bit verson of NAMD on Windows7

I have downloaded NAMD 2.9 for Win64-MPI. I downloaded the .zip file, extracted it and tried to run the program. But it gave the following error message "msmpi.dll file is missing". I am sure that...

12 December 2013 2,976 10 View

How to improve the performance by using NAMD for MD on windows OS?

I am using NAMD for MD on windows OS, using +p4 in "+p"On i5 processor uses 100 % CPU but not 100 % memory. How can we make 100% memory utilization?

11 November 2013 9,305 2 View