[gmx-users] Negative arginine?
feenstra at few.vu.nl
Tue Nov 30 17:28:41 CET 2004
Steven Spronk wrote:
> What I'm wondering, though: is it at all reasonable to keep all the atoms
> there--just change the charges in the molecular topology file so that the
> charge group on the side chain now has a total charge of -1 instead of +1?
> All the bonding terms and the LJ terms would remain the same; only the
> electrostatic interations would change.
IMHO, it is not reasonable at all. You'd want a 'physical system' that
could at least in principle correspond to a real state, which in your
proposed case you clearly have not. What kind of 'control' simulations for
your WT (as per your previous mail) did you have in mind?
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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