<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>Sorry for the delay answering. These questions are better put on the GROMACS users list. </div><div><br></div><div>1) Yes -- the Berendsen barostat does not sample the correct distribution of pressures.</div><div>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).</div><div> </div><div><br></div><div><br><div><div>On Jun 8, 2009, at 3:02 PM, Mauricio Carrillo Tripp wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>I've been following directions at <a href="http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial">http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial</a><br>to calculate hydration free energies of a few small molecules, and I have a couple of questions:<br> 1) Is there a reason for using NVT instead of NPT for the production step?<br>2) I noticed that between the equilibration and the production runs you generate velocities at each step,<br> instead of using the ones from the previous step. Is there a reason for doing this? wouldn't this<br> 'de-equilibrate' an already equilibrated system?<br><br>Thank you.<br clear="all"><br>-- <br> 0 | Mauricio Carrillo Tripp, PhD<br> / | Department of Molecular Biology, TPC6<br> 0 | The Scripps Research Institute<br> \ | 10550 North Torrey Pines Road<br> 0 | La Jolla, California 92037<br> / | <a href="mailto:trippm@scripps.edu">trippm@scripps.edu</a><br> 0 | <a href="http://www.scripps.edu/~trippm">http://www.scripps.edu/~trippm</a><br> <br>** Aut tace aut loquere meliora silentio **<br></blockquote></div><br></div></body></html>