Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?

From: case <>
Date: Tue, 13 Apr 2010 07:59:04 -0400

On Tue, Apr 13, 2010, Jianing wrote:

> but maybe I have found the reason for this surprising phenomenon, and I
> need you to give a juge on this.
> you know, writing every 4fs for 3.5ns is a very large mdcrd file,
> especially when the trajectory is not a binary file, so I just cut
> it into hunderds of pieces. That is, when sander finishes every 10ps
> interval,it will output md1.rst, then, when do the next 10ps, the
> initial coordinates is from md1.rst. and this cycle lasts until 3.5ns is
> reached. Although this is proceeded by computer automatically, this may
> also bright in errors, because the data accuracy is different between
> calculating and reading data in sander, which I didn't know before.

OK -- my bet is that you are seeing the Langevin problem, since you are using
ntt=3. You *must* use a different random number each restart (or set ig=-1).

  author = {Sindhikara, D.J. and Kim, S. and Voter, A.F. and Roitberg, A.E.},
  title = {{Bad seeds sprout perilous dynamics: Stochastic thermostat induced
trajectory synchronization in biomolecules}},
  journal = {J. Chem. Theory Comput.},
  volume = {5},
  pages = {1624-1631},
  year = {2009}

and earlier articles referred to there.

[developers: is there any good reason we should make the default value be
-1 for ig?]

...good luck.....dac

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Received on Tue Apr 13 2010 - 05:00:04 PDT
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