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...

08 September 2019 7,110 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...

09 October 2015 5,358 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...

11 December 2014 1,828 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...

10 November 2014 3,978 5 View

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

08 September 2014 2,551 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...

05 June 2014 5,719 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...

04 May 2014 5,403 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...

11 December 2013 2,920 10 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

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

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

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

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

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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View