[gmx-users] Extracting Trajectory and False Simulation

[Tsjerk Wassenaar]

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.