[gmx-users] constrainig counterions

[Anton Feenstra]

aswin narain wrote:
> How do I constrain the movement of counterions using gromacs?

You can put position restraints on them, but then your solute (e.g. protein)
can still move away from its initial position.

Distance restraints could do the trick, but then you will first have to
merge the topologies of your solute with that of your counter-ions.
The reason is that in Gromacs, disres are bonded interactions and thus
can only occur within one molecule. Since there are no bonds between
the solute and the ions, this will be as trivial as adding the lines of
[ atoms ] of the ions to the [ atoms ] of the solute.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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 chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|