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

From: Adrian Roitberg <>
Date: Wed, 8 Jul 2009 00:18:21 +0100

I still need to think a bit about the 'bug' and possible solutions but....

There is a particular problem when using ntt=3 (langevin) and this
ntr/nscm issue.

Langevin translates AND rotates the molecule without a flying block of
ice problem, it does it because it MUST do it due to the random forces.

Then, if you have the whole system under ntr=1 control, it does not
really matter, ntr basically does not allow COM changes.

Now, if you have a system like Ross', with only some residues
restrained, you can see the problem !

The restrained part does not really move. But, the unrestrained part
under langevin dynamics, can and should move its own COM (truly, the
complete system's COM !).

This creates strong problems...

A possible solution is to not allow ntr=1 and langevin...

case wrote:
> On Tue, Jul 07, 2009, Ross Walker wrote:
>> So it looks like nscm is getting set to 1000 both in sander and pmemd
>> regardless of the value of ntr.
>> This seems to run the nucleosome run nice and stable with the behavior I
>> expect. Anyone got any comments?
> 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
> 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.
> My vote is to just enforce nscm=0 when ntr=1. 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.
> ...dac
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> AMBER-Developers mailing list

                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
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Received on Tue Jul 07 2009 - 18:10:09 PDT
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