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

Marc Baaden baaden at smplinux.de
Sun Jun 5 18:24:44 CEST 2005

Hi David,

>>> David said:
 >> 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.

thanks for the suggestion. I tried it and indeed this seems a clear source
of energy drift. I observe the following tendency:

timestep  energy drift (over 10 ps)
--------  ------------
0.1 fs    - 0.04 kJ/mol
0.2 fs    - 0.15  "
1   fs    - 4.0   "
2   fs    - 11.7  "

I'd be tempted to conclude that constant energy simulations would thus be
rather utopic for any protein/peptide system bigger than a couple of
residues and aiming at roughly nanosecond timescale. Or are there other
tricks that would work (eg dummies .. but I think they'd only buy an
order of magnitude) ?

On the other hand I guess for selected system types (like the water cluster
you describe) it does work.

Thanks, Marc

 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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