Hi,
Sorry for the delay answering. These questions are better put on the
GROMACS users list.
1) Yes -- the Berendsen barostat does not sample the correct
distribution of pressures.
2) Regenerating velocities is fine for a couple of reasons: (a) we are
after thermodynamics, not dynamics, and (b) regenerating velocities
does not de-equilibrate the system (see the Andersen thermostat, for
example).
On Jun 8, 2009, at 3:02 PM, Mauricio Carrillo Tripp wrote:
Hi,
I've been following directions at
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial
to calculate hydration free energies of a few small molecules, and I
have a couple of questions:
1) Is there a reason for using NVT instead of NPT for the production
step?
2) I noticed that between the equilibration and the production runs
you generate velocities at each step,
instead of using the ones from the previous step. Is there a
reason for doing this? wouldn't this
'de-equilibrate' an already equilibrated system?
Thank you.
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | tri...@scripps.edu
0 | http://www.scripps.edu/~trippm
** Aut tace aut loquere meliora silentio **
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