[gmx-users] Extracting Trajectory and False Simulation

[Rabindra Raj Oliya]

Thank you for your kind suggestions
But how how can I use my alternative topology file in mdrun -rerun? I found no option to include topol.top in the synopsis you mentioned.



Rabindra Raj Oliya

-------- Original message --------
From: Tsjerk Wassenaar <tsjerkw at gmail.com> 
Date: 07/09/2015  11:57 AM  (GMT+05:45) 
To: Discussion list for GROMACS users <gmx-users at gromacs.org>,Rabindra Raj Oliya <oliyarabindra at gmail.com> 
Subject: Re: [gmx-users] Extracting Trajectory and False Simulation 
 
Hi Rabindra,

You can do an mdrun -rerun with the original trajectory and the alternative topology.

Cheers,

Tsjerk

On Mon, Sep 7, 2015 at 6:32 AM, Rabindra Raj Oliya <oliyarabindra at gmail.com> wrote:
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

--
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.



-- 
Tsjerk A. Wassenaar, Ph.D.