RE: [AMBER-Developers] Possible bug with ntt=3 and ntr=1 - Possible Fix for PMEMD.

From: Ross Walker <>
Date: Tue, 7 Jul 2009 23:58:09 +0100

Hi Dave,

> Why is repositioning necessary at all if you have restraints? Plus,
> your idea
> doesn't seem to take into account restarts -- if you've been changing
> the

You would think so except for the nucleosome I see serious instabilities. In
this case I allow the protein to move but the surrounding DNA is fixed with
restraints. The two are not covalently bonded and the net result is the
center 'yolk' just gets shaken like crazy and the whole thing (excluding the
DNA) just falls apart. It seems to be a subtle issue but I think it is also
related to how much of the system is restrained. In the case f the
nucleosome it is as if the system just keeps being given a net force in one

> reference coordinates on the fly, you'd have to write them out
> somewhere in
> order to be able to restart. But "reference coords are just that: a
> reference
> that should not change.

Yes I can see how that would be a problem here. Or rather we would need to
store the total displacement by which the coordinates were shifted in the
restart file.

> My vote is to just enforce nscm=0 when ntr=1.

Okay, I will update pmemd to do this as well. I'll put in the fix for
re_position as well though just in case we change our minds.

> However, I can't
> reproduce your
> report using sander: if I set ntr=1 in a gb calculation, nscm is
> printed out
> as 9999999, not 1000. So, you might want to do some quick debugging
> here.

This is because for sander I used AMBER 10 which does not enforce this. Thus
we should perhaps consider a bugfix for AMBER 10 to add this code?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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Received on Tue Jul 07 2009 - 18:09:49 PDT
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