[gmx-users] Different Results with Different Platforms

[Justin Lemkul]

On 10/6/16 7:13 AM, Kelechi Okoroafor wrote:
> Thank you for the tip, Justin.
> I incorrectly thought that the coordinates and box dimensions were
> sufficient to preserve the pressure of the system.
> I shall make a habit of restarting simulations with the checkpoint file
> rather than .gro files.
>
> My sequence of commands were:
>
>
>    - gmx  grompp  -f npt.mdp   -c EM.gro   -p sys.top   -o NPT1.tpr  -n
>    index.ndx   -maxwarn  -1
>
>    -
>
>    gmx  mdrun -v -deffnm NPT1  -nb gpu -tunepme
>    -
>
>    gmx editconf -f  NPT1.gro  -o   NPT1.pdb  -c -d 0.00
>    -
>
>    gmx editconf -f  NPT1.pdb  -o   NPT1.gro  -c -d 0.00
>    -
>

If you just want to convert file formats, omit -c -d in your editconf command 
and nothing will change.  By using -d 0.00, you will be adjusting the system 
size (you will see this by comparing the box vectors in the input and output 
files).  You're ensuring a bad discontinuity by doing this.  My recommendation 
is to always use unmodified files when continuing runs; it's basically 
bulletproof.  If you want a different format for visualization, that's fine, but 
just use it for visualization.  Your original NPT1.gro should have been fine, 
but having transformed to .pdb while manipulating the box, then back, you're 
just invalidating anything that was done previously.

-Justin

>    gmx  grompp  -f pme.mdp   -c NPT1.gro   -p sys.top   -o NVT1.tpr  -n
>    index.ndx   -maxwarn  -1
>    -
>
>    gmx  mdrun -v -deffnm NVT1  -nb gpu -tunepme
>
>
>
>
>
>
>
>

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

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

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