[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

Alan 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.

And Chris:

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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