Send me the prmtop and starting coordinates, Gerald. We've got a similar
case here: big system, but could contain some bad bond stretches and
unresolvable tangle that gets lost in the milieu.
Dave
On Fri, Jul 15, 2016 at 3:56 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> quick question: have you used ParmEd to change the mass yet?
>
> Hai
>
> On Fri, Jul 15, 2016 at 3:54 PM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
> > Hello,
> >
> > I have a protein system in water (321,300 atoms including ~100,000 water
> > molecules). I'm trying to use Hydrogen Mass Repartitioning (HMR) to
> > benefit a 4 fs timestep. However, it seems to fail. dt = 0.002 is OK,
> > but with dt = 0.003, the temperature goes bad after a few thousands
> > steps, and with dt = 0.004, it's even faster. This is for pmemd.cuda
> > with Amber16 (all last patches applied) as well as pmemd.MPI.
> >
> > The mdin file is:
> > &cntrl
> > imin = 0, ntx = 5, irest = 1,
> > dt = 0.004, nstlim = 1000000,
> > ntb = 1,
> > ntt = 1, ig = -1, temp0 = 300.,
> > ntc = 2,
> > ntpr = 1000, ntwx = 10000, ntwv = 00, ntwe = 10000,
> > /
> >
> > From the mdin of the GPU benchmark, I've also tried to add tol =
> > 0.000001 as well as ntf = 2. No improvement.
> >
> > Any idea?
> >
> > Gerald.
> >
> > --
> >
> >
> ____________________________________________________________________________
> >
> > Prof. Gerald MONARD
> > SRSMC, Université de Lorraine, CNRS
> > Boulevard des Aiguillettes B.P. 70239
> > F-54506 Vandoeuvre-les-Nancy, FRANCE
> >
> > e-mail : Gerald.Monard.univ-lorraine.fr
> > tel. : +33 (0)383.684.381
> > fax : +33 (0)383.684.371
> > web : http://www.monard.info
> >
> >
> >
> ____________________________________________________________________________
> >
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Received on Fri Jul 15 2016 - 13:00:04 PDT
