Thanks dear Chris and Berk. 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.
Thanks Berk for explaining about the Kinetic energy. And Chris: On Tue, Jul 27, 2010 at 15:57, <[email protected]> wrote: > Dear Alan: > > (although you should try gromacs compiled in double precision). > I did, same results. > I can reproduce the non-zero kinetic energy with a single spc water, > as long as I add define=-DFLEXIBLE to the .mdp file. The output .gro > contains all zeroes for velocities (as long as the input .gro does not > contain any velocities!): > I was hoping that my error would be something simple like forgetting "define=-DFLEXIBLE", but adding that made no difference yet. > I added unconstrainted_start=yes to your .mdp file but that did not help. > I am using GMX 4.0.5 and if I add "unconstrainted_start=yes" I got a error: WARNING 1 [file SPE.mdp, line unknown]: Unknown or double left-hand 'unconstrainted_start' in parameter file I never heard about this option. I tried the same system in CNS/XPLOR and the results matched AMBER and NAMD. So far only GROMACS looks awkward. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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