[gmx-users] "ideal" mdp file for NVE simulation as textbook example

David spoel at xray.bmc.uu.se
Sun Jun 5 12:39:39 CEST 2005

On Sun, 2005-06-05 at 12:00 +0200, Marc Baaden wrote:
> Hi,
> I am currently preparing/improving a tutorial on MD which is based
> on Gromacs. One of the things would be to compare a "normal" run
> to a run where all is conserved as good as possible in an NVE
> ensemble, that is the energy should be as constant as possible.
> For this I have tried the attached mdp file, with infinite cutoff,
> no constraints and no P-/T-coupling. I run it in double precision.
> Still the energy goes down (ca 4 kJ per 10 ps) with increasing
> noise. (See http://www.shaman.ibpc.fr/nvetest.png at the bottom)

We have done quite a few simulations of water clusters in vacuum with
settle that give perfect energy conservation (of course there are small
fluctuations, but no trend like you have here). For these systems we are
lacking all the bonded interactions of course. Maybe you want to try to
reduce your time step to 0.2 fs (unless you have dummies). You should
then do the same simulation length (10 ps) and compare.

> Now I wonder whether this is as good as it gets, or whether I
> overlooked some other option to avoid numerical and algorithmic
> inaccuracies ?
> (I can't run PME, I am in vacuo and charged; the system is bpti)
> Thanks for any suggestions,
>   Marc Baaden
>  BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
>  FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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