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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Received on Tue Nov 29 2011 - 10:00:03 PST
