[gmx-users] "ideal" mdp file for NVE simulation as textbook example
baaden at smplinux.de
Sun Jun 5 18:24:44 CEST 2005
>>> 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.
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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