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

[Justin A. Lemkul]

Alan wrote:
> 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 
> <mailto: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.
>  

Typo: the option "unconstrained_start" should be replaced by "continuation" in 
the 4.0.x series; grompp will replace it for you if the old option is present.

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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