[gmx-users] "ideal" mdp file for NVE simulation as textbook example
spoel at xray.bmc.uu.se
Sun Jun 5 19:06:39 CEST 2005
On Sun, 2005-06-05 at 18:24 +0200, Marc Baaden wrote:
> 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) ?
If you increase the tolerance for shake or LINCS you could also use
constraints. The question of course is whether there is any part of the
potential that is especially prone to energy drift.
> On the other hand I guess for selected system types (like the water cluster
> you describe) it does work.
Which proves that the integration algorithm is fine, and the nonbonded
energy functions too.
> Thanks, Marc
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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