[gmx-users] implicit solvent
baaden at smplinux.de
Thu Nov 7 10:32:40 CET 2002
>>> Erik Lindahl said:
>> The lack of viscosity is both a feature and a problem; it makes some
>> large-scale motions occur 10-15 times faster, but this of course means
>> we cannot draw conclusions about timescales of the dynamics anymore. We
>> might have to include a stochastic integrator that adds some drag to
>> atoms exposed to the (implicit) solvent...
Yes indeed. The initial tests with a simple implicit model showed just that.
You absolutely need a stochastic integrator to get meaningful behaviour
of your system (in my case a protein/membrane in impl. water).
But, there is already a stochastic integrator in Gromacs. Does this mean
that the implicit solvent won't work with all gmx integrators by default ?
Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
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