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

[Mark Abraham]

... and the result can look even more different if the two runs used
different numbers of domains (e.g. because they were run on different
hardware in the default mode of mdrun).

Mark

On Thu, May 5, 2016 at 1:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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