PS the *simplest* thing you can do, and you can do it right now, is set
ntpr to 1, and run for 200 cycles. Then send me both mdouts, appropriate
labelled...
Scott
On Tue, Nov 29, 2011 at 9:51 AM, Scott Le Grand <varelse2005.gmail.com>wrote:
> The best way to get this addressed is to get a solid repro in Mark's hands
> so he can test if it's something inside CHAMBER, and then if not, hand it
> over to me.
>
>
> On Tue, Nov 29, 2011 at 7:07 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com> wrote:
>
>> 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
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
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>>
>
>
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Received on Tue Nov 29 2011 - 10:00:04 PST
