[gmx-users] regarding confout.gro

[RINU KHATTRI]

hello justin
i have been visualized the file of confout.gro file in vmd and the
position of protein and ligand is ok i know i have to analyze all the
parameters like energy and rmsd is it sufficient to extend my
simulation or which file i have to visualized

On Tue, Oct 14, 2014 at 5:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/14/14 12:31 AM, RINU KHATTRI wrote:
>>
>> hello gromacs user i am working on protein ligand complex with popc
>> membrane
>> i am running production md in extended time (40 ns) i got some file i
>> am using -noappend option i got confout.gro file in each extended time
>> what is the use of this file if i want see my protein or ligand are in
>> proper place this confout.gro is sufficient of i  have to see traj
>> file
>
>
> The confout.gro file is simply the last snapshot of the simulation interval.
> Whether or not it is reflective of the dynamics during that interval is
> unknown without doing analysis and simple visualization.
>
> -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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