[gmx-users] simulation Self assembly monolayers with OPLS-TIP3P (CPU and GUP)

[Justin Lemkul]

On 5/4/16 11:40 PM, Pratiti Bhadra wrote:
> Dear All,
>
> I am having a problem with OPLS FF.
>
> If I simulated SAMs layer with only water layer (without any peptide and
> protein) using OPLS-AA + TIP3P in GPU system that simulation is simulated
> properly there is no problem. But if the same system I run using MPI
> (parallel gromacs) then water molecules are penetrating SAMs layer going
> toward Sulfure atoms and make a whole in SAM layer. I am confused why both
> system is giving me separate result? I want it to run in MPI.
>
> Can anyone solve this problem?
>

Different simulations can produce different results, hence why replicates are 
typically used to confirm the observed behavior.

-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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