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
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue Jan 14 2003 - 16:55:14 PST
