AMBER Archive (2003)

Subject: Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sat Aug 23 2003 - 09:41:42 CDT

Chen -
I did some additional checks of the source, and still don't see problems in
terms of sander 6 - pmemd 6 conformance. A dump of force array components
(ie., force vectors for each individual atom) attributable to the two
executions of the dihedral code in the first step are identical to 5 places
after the decimal for a 20943 atom problem (the relevant part being 795
protein atoms). This typically constitutes at least 6digit precision, and I
did not check for higher levels of conformance. For my code, dihedrals are
handled the same way in sander 6 mode and sander 7 mode. For sander, I
think the mechanisms are supposed to be the same. However, the dihedral
code in 7 has been modifed; specifically the 1-4 NB code has been pulled out
of the dihedral routine and placed in the ewald code. Tom Darden would have
to comment on whether there are any differences in how this code behaves
(ie., a subtle difference between sander 6 and 7 is possible here, and pmemd
would track the 6 behaviour).
Regards - Bob

----- Original Message -----
From: "Chen, Ya" <ya.chen_at_roswellpark.org>
To: <amber_at_scripps.edu>
Sent: Saturday, August 23, 2003 12:47 AM
Subject: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7

> Hi, everyone,
>
>
>
> I did a short run (<1ns) for a system of a small peptide in TIP3P water
box using both pmemd and sander7 and found that the restart structures from
equilibration (minimization followed by 75ps md) by pmemd and sander7 were
quite different. The difference was maintained throughout production runs.
Pmemd did not disrupt the molecule as much as sander7 when RMSDs are
considered. But when examining individual residues, I found that for some
residues, (Gly-Arg, in a beta-turn,) pmemd set disallowed (in Ramachandran
plot) phi-psi values while phi-psi’s from sander7 are more allowed. By the
end of the simulation, those disallowed phi-psi’s were not changed yet.
>
> My questions:
>
> Is it normal that some torsion angles are disallowed throughout
simulation?
>
> What is the possible cause of the inconsistency between pmemd and sander7
for my system?
>
>
>
> The system was created with ff99 (Amber7) and temp=300 in production runs.
The input files are identical. The starting structure (before minimization)
was resolved from NMR spectra, without disallowed torsion angles.
>
> Thanks for your help.
>
>
>
> Chen
>
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