[gmx-users] free energy calculation in a big system

Markus O Kaukonen mokaukon at cc.helsinki.fi
Tue Aug 31 11:42:25 CEST 2004

Dear All,

Never done any free energy calculation with a computer, so... :

Is it possible (cpu and otherwise) to do a free energy calculation for a
system like in the manual (v 3.2 manual) page 36, fig. 3.9 case B
ie. two different inhibitors (I and I') docking the same enzyme (E)
when I and I' differ by one H+ (and the partial charges in I and I' are

I (one system) and I' (the other system) have about 200 atoms and
E has 70000 atoms.

It seems at least that one has to do lot of things by hand in the topology
file (for things related to those 200 atoms).

Terveisin, markus.kaukonen at iki.fi

-----------www= http://www.iki.fi/markus.kaukonen---------------
Markus.Kaukonen at helsinki.fi   \ HOME->   Verajakallionkatu 6 a 5
Helsinki Bioenergetics Group   \_______  02600 Espoo, Finland
Institute of Biotechnology             \ tel:+358-(0)9-5127122/h
Biocenter 3, P.O.BOX 65 (Viikinkaari 1) \____
FIN-00014 University of Helsinki              \______ H+ ______
tel: +358-(0)9-19159752/o, fax: +358-(0)9-19159920             \
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---

More information about the gromacs.org_gmx-users mailing list