[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition
alanwilter at gmail.com
Tue Jul 27 17:36:28 CEST 2010
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.
On Tue, Jul 27, 2010 at 15:57, <gmx-users-request at gromacs.org> 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.
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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