[gmx-users] skipping the EM, NPT and NVT for re-run

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 4/24/14, 4:29 PM, Saman Shahriyari wrote:
> you mean i should expect a different trajectory every time i do the simulation
> under the same conditions?!

It's certainly possible.

http://www.gromacs.org/Documentation/Terminology/Reproducibility

One of the many reasons why a single trajectory is often insufficient to make 
substantive claims.

-Justin

> On Wednesday, April 23, 2014 4:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/23/14, 2:04 AM, Saman Shahriyari wrote:
>  >
>  >
>  >
>  >
>  > dear users
>  > i have an old simulation witch is not working properly. is there anyway i can
> re-run the simulation using the before md .tpr file, the .gro file and the
> current .xtc?
>
>
> If you have the .tpr file, that's all you need.  You can just re-run it and
> produce a new .xtc file, though of course there is no guarantee that it will be
> identical to the original one.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================