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 - 13:00:02 PDT
