It would be great if the pmemd.cuda people (Ross, Scott?) could confirm
that pmemd.cuda has indeed not been tested with the combination of a
CHAMBER prmtop and NPT.
Is this assumption true?
And, will there be efforts to test this and iron out potential
bugs/problems?
As I'm expecting my system to change conformation, I would really prefer to
run the production MD with NPT (as opposed to NVT after NPT equilibration).
It would be a pity if I need to do (expensive) multi-CPU pmemd.MPI runs
instead of using the superspeedy pmemd.cuda on a single GPU card...
If this would be helpful, I'd be happy to try and set up some small
test-systems (e.g. alanine dipeptide in waterbox) and see if I can
replicate the problem.
Thanks,
Marc
On 24 November 2011 17:16, Marc van der Kamp <marcvanderkamp.gmail.com>wrote:
> Hi Mark,
>
> Thanks for your input!
> Unfortunately, pmemd.cuda doesn't support the do_charmm_dump_gold option
> of the debugf namelist. So I can't compare the forces this way.
> This may indicate that pmemd.cuda has never really been tested (fully)
> with CHAMBER prmtops...
>
> Thanks,
> Marc
>
>
> On 24 November 2011 13:30, Mark Williamson <mjw.mjw.name> wrote:
>
>> On 11/24/11 12:20, Marc van der Kamp wrote:
>> > To provide more info:
>> > I've just finished running 1ns of NVE and NVT MD with pmemd.cuda, and
>> they
>> > DON'T give the issue described, with CA RMSD < 1.8 in 1ns simulation.
>> > The problems therefore appear to arise with a combination of pmemd.cuda,
>> > NPT (ntb=2, ntp=1) and (my) CHAMBER prmtop.
>> > I would prefer to run this system with NPT, as a conformational change
>> may
>> > occur. Nothing as large as unfolding though, just a small part of the
>> > protein opening up. I'm using a fairly large water box around the
>> protein,
>> > so perhaps NVT would still be ok for this. Any comments appreciated!
>> >
>> > --Marc
>>
>>
>> Dear Marc,
>>
>> I'm not sure where the source of this issue lies at the moment, but I
>> have initial debug route to narrow this down.
>>
>> Have you tried checking that the potential energy and resultant per atom
>> forces of the first step between two identical runs in pmemd and
>> pmemd.cuda are the same?
>>
>> The "do_charmm_dump_gold" option can be used for this:
>>
>> &debugf
>> do_charmm_dump_gold = 1
>> /
>>
>> and will dump the following:
>>
>> NATOM 24
>> ENERGY
>> ENER 0.6656019668295578D+02
>> BOND 0.1253078375923905D+01
>> ANGL 0.3101502989274569D+01
>> DIHE -0.2481576955859662D+02
>> VDW 0.3170732223102823D+01
>> ELEC 0.8385065265325110D+02
>> FORCE
>> 1 0.1774846256096088D+00 -0.7072502507211014D+00
>> 0.6898056336525684D+00
>> 2 -0.2664878707118652D+00 -0.2989897287348136D+00
>> -0.4514535076187112D+00
>> 3 0.1307432194682785D+00 0.1309127935015375D+01
>> 0.1002524982820262D+01
>> ...etc..
>>
>>
>> There are more examples in $AMBERHOME/AmberTools/test/chamber/dev_tests
>> and also have a look at p 41 of http://ambermd.org/doc11/AmberTools.pdf
>> When I was implementing this, I was using these tests to ensure that I
>> was getting the same potential energy and per atom forces from the AMBER
>> md engines as I was from the charmm MD engine for the same system.
>>
>> This test could be used to see if there is a difference in forces
>> between pmemd and pmemd.cuda MD engines. If the issue is not here, one
>> may need to look into the integration within this ensemble.
>>
>> Regards,
>>
>> Mark
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Nov 29 2011 - 07:30:04 PST
