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 - 13:00:03 PDT
