[gmx-users] Perturbation from/to dummies

[Anton Feenstra]

Ing. Vojtěch Spiwok wrote:
> Dear GMX developers/users
> 
> Do you know about some source of information how
> to do free energy perturbation from dummies to real
> atoms and back (eg. aminoacid mutations) ? In the
> manual I found only how to perturb from atom to atom.

A dummy in this context simply is an atom without interactions.
The trick is to make an atomtype with 0 charge and 0 LJ parameters,
and perturb you 'normal' atom to this atom type.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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