[gmx-users] free energy calculation

[Anton Feenstra]

Tony Zhou wrote:
> Dear All,
> 
> I am a quite new user for Gromacs so I really appreciate your helps.
> 
> I am dealing with the free energy calculation for two enantiomers. For that
> I need to change H(connected to CA) to CH3 for one molecule and other way
> around for another molecule, but such H is not included in the topology file
> of Gromacs.  Just wonder how to define/add it in the library. Is there any
> standard protocol to set up the free engergy calculation in GROMACS? The
> description in Gromacs mannual is not so clear to me even I checked the many
> discussions in the mailing list.

Hi Tony,


If you look in the files for the ffgmx2, you will find it has explicit
aliphatic hydrogens added that only have mass, no LJ and no Coulomb
(i.e. c6, c12 and q are all zero). It would be trivial to add this
atom type to the forcefield you are now using, and use that for your
hydrogen. That would also introduce the least deviation from the
original molecule topology. This H can be easily transmuted into a -CH3
united atom. Be aware that there may be an entropy correction needed
for the addition of the new H atom in your molecule (check with
literature, I am no expert in this, or maybe somebode else can fill in?).


-- 
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)                               |
|_____________|_______________________________________________________|