AMBER Archive (2003)

Subject: Re: nscm

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 14 2003 - 18:55:14 CST

On Tue, Jan 14, 2003, Kristina Furse wrote:
>
> I've been running a large explicit simulation on a protein with periodic
> boundary conditions, PME, and the works for almost 2ns, now, with nscm=0
> (turning off removal of translational center of mass movement) the whole
> time. It has just been brought to my attention that that was probably a bad
> idea. Are there long term implications for not using nscm? Would it be
> advisable to turn it on now, midstream, or would it be better to handle any
> translational drift with post-processing? (I say midstream, but I only
> intend to collect for another 500-700 ns.)
                                        ^^

Pretty ambitious, that. :-)

Yes, turn on nscm, at least for a short test run. The first time it is
triggered it will print out how much energy has gone into translational
motion. This should be a negligable amount (depending mostly on what you have
used for ntt and tautp). But at least you will know what is happening.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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