[gmx-users] Re: NVE problems in gmx-users digest, Vol 1 #1174
spoel at xray.bmc.uu.se
Tue Jan 6 20:29:01 CET 2004
On Tue, 2004-01-06 at 17:04, istvan at kolossvary.hu wrote:
> A good way of testing energy conservation is using delta_E = log(1/N *
> Sum|(Ei-E0)/E0|), see JCP 103, 1995, 9444-9459. Ei is the current total
> energy, E0 is the initial total energy and N is the number of sample points
> on the stretch of the trajectory considered. delta_E < -2.5 is indicative of
> a stable constant energy simulation. With the above settings I was able to
> keep delta_E below -2.5 for 33 ps. I guess this can be good or this can be
> bad depending on your perspective. As far as I am concerned I am rather
> disappointed that after only 33 ps the simulation should be considered
> unstable. Can anybody comment on
> 1. Whether I missed something and even more conservative settings should be
> used for NVE,
> 2. It concerns me a lot that we typically run hundreds or thousands of
> picoseconds with T/P coupling whereas the underlying integrator cannot
> conserve energy beyond a few tens of picoseconds.
Have you tried LJ different from switch, e.g. cut-off?
> Many thanks,
> Istvan Kolossvary
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David van der Spoel, PhD, Assist. 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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