[gmx-users] Extracting Trajectory and False Simulation

[Rabindra Raj Oliya]

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

-- 
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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
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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