Hello,
On 07/15/2016 09:56 PM, Hai Nguyen wrote:
> quick question: have you used ParmEd to change the mass yet?
>
Yes. I forgot to say: I've modified the topology file with the
HMassRepartition command in parmed and I have tested both the "normal"
repartioning and the "dowater" option. Same results.
Gerald.
> 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
>>
>>
>> ____________________________________________________________________________
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
____________________________________________________________________________
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
____________________________________________________________________________
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 15 2016 - 14:30:02 PDT
