Hello,
This is the main issue in one sentence:
When I run NPT MD of a protein with pmemd.cuda and a CHAMBER prmtop, CA
RMSD rises quickly and enormously (>10 Ang in ~100 ps), whereas this does
NOT occur with pmemd.MPI.
I am running a protein-ligand system using the CHARMM force field.
I'm using AMBER11/AmberTools1.5, with the latest patches for pmemd.cuda
(bugfix.17)
I created the prmtop using CHAMBER from a CHARMM psf file.
I have noticed before that when one is using multiple chains with residue
numbers being reset to 1 in new chains, CHAMBER makes some 'mistakes' (see
e.g.
http://archive.ambermd.org/201104/0417.html), i.e.
- the 1st water molecule is lumped in with the last solute residue/molecule
(a ligand in this case), so the RESIDUE_LABEL and RESIDUE_POINTER sections
miss out on this water and need to be adjusted.
- ATOMS_PER_MOLECULE are incorrect because of the same reason.
To avoid this behaviour, I used a simple workaround: I modified the CHARMM
psf first to have all residues in the same segment ("ALL") and numbered
them sequentially. (I still need to manually fix SOLVENT_POINTERS.)
Thereafter, I started running simulations with the created CHARMM prmtop
files.
I first ran a short equilibration protocol on CPUs, essentially consisting
of heating the system and doing some NPT equilibration with positional
restraints on the CA atoms, and subsequently gradually releasing the
restraints.
Thereafter, I started running NPT langevin dynamics (ntb=2, ntt=3).
Something I've noticed a little too late is that when using pmemd.cuda_SPDP
(on a single GPU), the total and potential energies take a nosedive in the
first few steps (something I haven't noticed before for other systems with
exactly the same inputs but using AMBER prmtop files): Etot is ~1400
kcal/mol lower and EPtot ~1000 kcal/mol lower in just ~150 steps (3ps).
Furthermore (probably in response), the CA RMSD of the system rises really
quickly, reaching 10 Ang after ~100 ps and 20 Ang within 400 ps (this is a
~300 residue protein) - essentially the protein is 'denatured' in just a
few 100 ps.
As mentioned before, when I run the exact same input with the exact same
system but with pmemd.MPI, total and potential energy stay near the value
after equilibration and RMSD develops 'normally' (stays below 2 Ang in
1000ps)
What could be the cause of this? Can it be due to a bug in pmemd.cuda when
handling CHAMBER prmtops?
Many thanks,
Marc
PS I'm currently running tests with pmemd.cuda_SPDP with modified input,
essentially the equivalent NVT and NVE simulations.
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Received on Thu Nov 24 2011 - 02:30:02 PST
