[gmx-users] charged proteins

Marc Baaden baaden at smplinux.de
Fri Mar 8 12:17:27 CET 2002


thanks for this very interesting discussion .. I also want to throw
some questions in .. especially as I am running simulations on a
membrane protein in lipid/water with ions, right now with a 14/18
cut-off. So - unless I am wrong - reaction field is not an option due
to the system anisotropy.

Berk Hess said:
>> Even in pure water a plain cut-off will give terrible artifacts.

Maybe I haven't looked hard enough at my system yet, but I haven't
noticed huge artefacts, so far everything is quite reasonable. so
what kind of artefacts should I be looking for ?

(And by the way is there any reference ? I do not mean the general
 PME vs cutoff things tested in a box of pure water, but something
 thoroughly tested on a more complex system, eg a water/lipid/ions


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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