[gmx-users] Negative arginine?

[Anton Feenstra]

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?

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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