Thanks dear Chris and Berk.<div><br></div><div>Indeed I contact Eric but still waiting a reply. BTW, the whole point I am trying here is to try to reproduce his results and apply to validate my application ACPYPE, which uses ANTECHAMBER.</div>
<div><br></div><div>Thanks Berk for explaining about the Kinetic energy.<br><br></div><div>And Chris:</div><div><br><div class="gmail_quote">On Tue, Jul 27, 2010 at 15:57, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div id=":410" class="ii gt">Dear Alan:<br>
<br>(although you should try gromacs compiled in double precision).<br></div></blockquote><div><br></div><div>I did, same results.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div id=":410" class="ii gt">
I can reproduce the non-zero kinetic energy with a single spc water,<br>
as long as I add define=-DFLEXIBLE to the .mdp file. The output .gro<br>
contains all zeroes for velocities (as long as the input .gro does not<br>
contain any velocities!):<br></div></blockquote><div><br></div><div>I was hoping that my error would be something simple like forgetting "define=-DFLEXIBLE", but adding that made no difference yet.</div><div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div id=":410" class="ii gt">
I added unconstrainted_start=yes to your .mdp file but that did not help.<br></div></blockquote><div><br></div><div>I am using GMX 4.0.5 and if I add "unconstrainted_start=yes" I got a error:</div><div><br></div>
<div><div>WARNING 1 [file SPE.mdp, line unknown]:</div><div> Unknown or double left-hand 'unconstrainted_start' in parameter file</div></div><div><br></div><div>I never heard about this option.</div><div> </div>
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I tried the same system in CNS/XPLOR and the results matched AMBER and NAMD. So far only GROMACS looks awkward.</div><div><br></div><div>Thanks,</div><div><br></div><div>Alan<br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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