[gmx-users] Extracting Trajectory and False Simulation

[João Henriques]

​The .top file is not useful for mdrun. It needs a .tpr that you create
using grompp, as you certainly had to do for the "ideal" simulation you
mention.

/J​

On Mon, Sep 7, 2015 at 8:36 AM, Rabindra Raj Oliya <oliyarabindra at gmail.com>
wrote:

> 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
>
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> --
> Tsjerk A. Wassenaar, Ph.D.
>
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