Adrian,
I've zipped the topology and the coordinates and they can be downloaded
at
http://filex.univ-lorraine.fr/get?k=w81rXhKkJovLn96ZzXv
I'm gonna check also with ntwx = 1.
Gerald.
On 07/15/2016 11:18 PM, Adrian Roitberg wrote:
> Gerald.
>
> If you share your files we can take a look on my group's side.
>
> We have seen this before due to a VERY weird issue. There are cases
> where tleap decides to create carbon chains going through the middle of
> a phenyl ring for instance. Incredibly enough, some of these are
> perfectly stable at 2 fs, even though they are wrong. 4 fs forces the
> issues and things blow up, but it has nothing to do with the time step,
> it is tleap's fault. I suggest you rerun with 4 fs and ntwx=1, and look
> at your trajectory to see what blows up.
>
>
> Adrian
>
>
>
> On 7/15/16 5:14 PM, Gerald Monard wrote:
>> 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
>>>>
>>>>
>>>> ____________________________________________________________________________
>>>>
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--
____________________________________________________________________________
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 - 15:00:03 PDT
