[gmx-users] Fwd: Issue with parallel simulations in vacuum

[Agusti Emperador]

Thanks very much Mark

In fact, the results that I find are pathological in the sense that the
kinetic energy does not seem to be correctly distributed along the system:
one of the proteins seems to be at much lower temperature than the other
one (according to their conformational sampling; they are disordered
proteins)

Best regards

Agusti



On Tue, May 16, 2017 at 4:19 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> In GROMACS 4.6.6 we added a fatal error for Andersen+constraints+domain
> decomposition with more than one domain, because it gave a temperature that
> is obviously too high. So, I presume Michael Shirts never implemented it to
> work / tested it with particle decomposition, either.
>
> Fortunately, 600 particles isn't likely to show an appreciable speedup for
> more than one rank, so I'd stay on a single rank, or update to a recent
> GROMACS and use Verlet + md + v-rescale.
>
> Mark
>
> On Tue, May 16, 2017 at 4:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/16/17 7:26 AM, Agusti Emperador wrote:
> > > Dear GROMACS experts,
> > >
> > > I am simulating a system of two disordered proteins in vacuum. I use
> > > gromacs 4.6.5. The serial simulation works fine, but when I run it in
> > > parallel (2 processors) it gives seriously pathological results.
> > >
> > > I use particle decomposition and periodic boundary conditions, because
> I
> > > want to simulate a solution at a certain concentration (technically,
> the
> > > simulation is in vacuum, but I have included the effects of solvation
> in
> > > the nonbonded terms of the force field in my coarse-grained protein
> > model).
> > > Each protein has 300 particles.
> > >
> > > I use exactly the same parameters and input files in the serial
> > simulation
> > > and in the parallel simulation. This is the mdp file that I use:
> > >
> > > integrator       =  md-vv
> > > dt               =  0.02
> > > nsteps           =  500000000
> > > nstxout          =  0
> > > nstvout          =  0
> > > nstenergy = 500000
> > > nstlog           =  500000
> > > nstxtcout        =  50000
> > > nstcomm = 1
> > > nstcalcenergy = 1
> > > xtc-precision    =  10
> > > rlist            =  1.4
> > > coulombtype      =  shift
> > > rcoulomb         =  1.2
> > > epsilon_r        =  15
> > > vdw-type         =  shift
> > > rvdw-switch      =  0.9
> > > rvdw             =  1.2
> > > tcoupl           =  andersen
> > > tc-grps          =  Protein
> > > tau-t            =  .1
> > > ref-t            =  300
> > > Pcoupl           =  no
> > > refcoord_scaling =  all
> > >
> > > It works perfectly in the serial simulation, but I need to make
> parallel
> > > simulations in order to simulate systems with many proteins.
> > >
> > > How could I solve the problem?
> > >
> >
> > What is the problem?  What do you define as "seriously pathological
> > results" in
> > this case?  Also note that 4.6.5 is practically prehistoric and you may
> > wish to
> > consider a newer, faster, less-buggy version of the code.
> >
> > -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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