[gmx-users] Different Results with Different Platforms

[Justin Lemkul]

On 10/5/16 9:46 PM, Kelechi Okoroafor wrote:
> Thank you very much, Justin.
> So I did not restart the simulation directly.
>
> One of my desktops had a hardware malfunction so I had to move my
> files between desktops.
> Before moving my files, I converted my final npt.gro trajectory into a
> .pdb file (for ease of vmd visualisation as vmd often crashes while
> viewing .gro files), then converted the files back to .gro to restart
> the simulation in a different desktop.
>
> Somewhere in between my file conversion, the trajectories must have
> been edited to cause such drastic pressure increase.
>

The difference between .pdb and .gro is negligible.  Not preserving the state by 
using the checkpoint basically negates any previous simulation as you will be 
restarting from a random state.  But without an exact sequence of your commands, 
it's pure guesswork and is unproductive for all involved.

-Justin

-- 
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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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