I'm guessing your issue is similar to the other one described on the mailing list today. Can you try creating a localized set of atoms (as in atoms that aren't far apart in simulation space) in each group of your COM mask and see if the simulation is stable?
Thanks,
Charlie
On 3/11/19, 8:13 AM, "David Bickel" <david.bickel.uni-duesseldorf.de> wrote:
Dear Prof. Case,
thank you for your kind reply.
> Just to be sure, are you up to date with code updates? In particular,
> have you applied update.7, which fixed a memory problem with COM
> restraints on GPUs?
I used Amber18.12 and Amber17.15 and was able to reproduce the described
problem in both versions.
> If so, see if using fewer atoms in the COM mask fixes anything.
My COM masks were well within, what is specified in the manual to work.
The mask :1 corresponds to 92 atoms, and @P31 to 94.
Still, I tried reducing the number of atoms. Reducing the number of
phosphor atoms to 32 (:PE.P31), did not solve the issue.
Reducing the number of atoms for the molecule in the membrane to 38
(:1.C=) initially seemed to solve the issue, but after ~1000 steps again
restraint energies overflowed and the system crashed.
Reducing the number of atoms for the molecule further to two
(:1.C21,C22), allows running the system on GPUs for several nanoseconds
without crashing or overflowing so far.
Still, I am troubled, because i do not see any rationale behind what is
working, and what is not.
I will send you my files and would appreciate you having a look into my
problem and probably shed some light onto what is going wrong here.
Best regards,
David
On 3/9/19 3:01 PM, David Case wrote:
> On Wed, Mar 06, 2019, David Bickel wrote:
>> I encountered a problem running simulations of a membrane system with
>> distance restraints on GPUs.
>> I used distance restraints (fxyz=0,0,1) between the
>> COM of the molecule (:1) and the phosphor atoms of the lipids (@P31), in
>> order to keep the molecule in the center of the membrane.
> It's certainly possible that some problem exists on GPUs with COM
> restraints, especially of the mask @P31 averages over lots of atoms.
>
> Just to be sure, are you up to date with code updates? In particular,
> have you applied update.7, which fixed a memory problem with COM
> restraints on GPUs?
>
> If so, see if using fewer atoms in the COM mask fixes anything. If that
> doesn't help, we'll probably need to get files from you to try to
> reproduce the problem.
>
> ...good luck....dac
>
>
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--
David Bickel
PhD Student
Computational Pharmaceutical Chemistry and Molecular Bioinformatics
Heinrich-Heine-Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Universitätsstr. 1
D-40225 Düsseldorf
Germany
Office: 26.23.00.22
Phone: +49 211 8112528
URL: http://cpclab.uni-duesseldorf.de
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Received on Mon Mar 11 2019 - 09:00:02 PDT
