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 - 06:00:03 PST
