[gmx-users] g_lie

[Anton Feenstra]

Filipe Maia wrote:

> I'm completly new to gromacs and i'm trying to do some free energy 
> calculations.
> I think that to use g_lie i need to make a run like the on in the 
> GROMACS Tutorial
> for Drug – Enzyme Complex and then run g_lie on the output energy file.
> Is this correct?

You'll need two runs: one of the 'free' ligand in water, and one of the
ligand bound to your enzyme. Be aware that one of the previous releases
of Gromacs contained an error in g_lie making it virtually unusable. Check
the archives for messages from me describing the problem and a possible
fix. Or, install 3.2 instead, that is already fixed.


-- 
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)                               |
|_____________|_______________________________________________________|