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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Received on Thu Nov 24 2011 - 09:30:03 PST
