AMBER Archive (2003)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 25 2003 - 16:33:38 CDT

Chen -
Thanks for following through on this, and sharing the results. I am very
happy that PMEMD in amber 7 compatibility mode is giving you essentially the
same results as sander 7. My comment on preferring to compare pmemd in 6
mode to sander 6 has to do with knowing that pmemd is a complete
reimplementation of 6, and should produce virtually identical results,
within the limits posed by roundoff errors in the math, which of course
results in trajectories that diverge rather quickly (all the calculations
are logically the same, but perhaps done at different times on different
machines in slightly different ways, leading to roundoff errors). Seeing 7
mode produce essentially identical results on something like this is really
really nice, though.
Regards - Bob

----- Original Message -----
From: "Chen, Ya" <ya.chen_at_RoswellPark.org>
To: "Robert Duke" <rduke_at_email.unc.edu>
Sent: Monday, August 25, 2003 5:03 PM
Subject: RE: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7

> Bob,
>
> I just finished analyzing a 4ns run by PMEMD (all patched,
amber7_compat=1.) And you were right, the results closely resemble what
I've got from sander7. Evolution of RMSD is somehow slower than sander7,
but again, at that time sander7 wasn't patched with bugfix42 yet.
Furthermore, phi-psi angles are now largely distributed in allowed areas,
which overlap with most areas shown by sander7. I think I'd stay with
amber7_compat=1 because the results make more sense for my specifc system.
I am not sure everyone would agree with me, but under normal conditions, too
many disallowed torsion angles from sander6 just doesn't feel right. I
would like to know whether someone has exammed this issue with a larger
protein.
> Thanks for your help!
>
> Regards,
> Chen
>
> -----Original Message-----
> From: Robert Duke [mailto:rduke_at_email.unc.edu]
> Sent: Saturday, August 23, 2003 12:37 PM
> To: Chen, Ya
> Subject: Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7
>
>
> Chen -
> Sounds good. I would point out for everyone, though, that in doing
comparisons between pmemd and sander, what we will have the most luck with
in comparing results is comparing sander 6 and pmemd in 6 mode. I say this
because while pmemd 7 mode is meant to mimic sander 7 to the extent
practically possible, there are some "under-the-covers" differences in
sander 7, mostly involved with extra points support, that I didn't track
because I don't support extra points. Thus, Tom D. changed some stuff in 7
that may or may not be significant. I first encountered this when we
noticed a change in virials values for crosslinked molecules in sander 7;
turns out that that was due to a change in 7 in the computation of molecular
and atomic virials; Tom regards neither the 6 or 7 implementation as "more
correct", they are just different (basically in whether they treat two
molecules crosslinked by an additional bond as 1 molecule or 2, I believe).
Where the 1-4NB calcs get done is different; I don't know if there are
subtle differences in the results. So what I am saying is that there MAY be
some differences between sander 6 and sander 7 that have not been sorted
out, so that muddies up comparisons between pmemd in 7 mode and sander 7.
Pmemd is mostly a fast implementation of sander 6, with additional support
for some sander 7 features, the primary one being sander 7-style step
integration and default variables. If you do get significantly different
numbers again, and they are not simply attributable to trajectory sampling
issues, then I think it would be really good to see what sorts of results
you get out of sander 6. Regards - Bob
>
>

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