[gmx-users] Extracting Trajectory and False Simulation

Rabindra Raj Oliya oliyarabindra at gmail.com
Mon Sep 7 06:33:03 CEST 2015

Actually I have two topology files corresponding to ideal and real system.
Initially I have simulated using ideal topology.Now I have to false simulate using real topology as we have to ensemble average over the ideal configuration.

Rabindra Raj Oliya

-------- Original message --------
From: Justin Lemkul <jalemkul at vt.edu> 
Date: 07/09/2015  7:43 AM  (GMT+05:45) 
To: gmx-users at gromacs.org 
Subject: Re: [gmx-users] Extracting Trajectory and False Simulation 

On 9/6/15 9:54 PM, Rabindra Oliya wrote:
> Dear sir,
> I have to extract the configuration stored into the trajectory file and
> carry out the false simulation (in which we set up just one MD step and a
> 0.0 time step) using the topology file. How can be this done?

Why bother?  A single step in which no time passes leaves you with the same 
coordinates you started with, which presumably you already have.

If you want to extract coordinates from a trajectory into something you can 
visualize, use trjconv.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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