[gmx-users] solvation free energie calculations
craigswank at hotmail.com
Wed May 5 18:51:03 CEST 2004
I'm sorry. The I thought the web-site I'm talking about was from the
GROMACS page, but it is not. The url is:
Sorry. Maybe if I explained better someone could help me.
First I created a structure file and topology file of toluene from a pdb
file of phenylalanine. The .top file was then edited to that the B state of
the molucule is all dummy atoms. The toluene was then put in a water box
and an energy minimization was done. This minimization geve the massage
that is did not converge after 22 steps and so on. I got the energy from
this job using g_energy and the energy at each step is zero. I continued
anyhow by performing and equilibration and simulation at many different
lambda values. The energy for each of these runs is zero.
One thing that I noticed is that when I performed the energy minimization on
the solvated toluene is that when the program told be it failed to converge
it also gave an energy. I'm not sure what this energy is compared to the
energies you get for each step using g_energy. It makes me wonder, though,
if g_energy is the problem (or more likely, my mis-use of g_energy).
Anyway, I would really appreciate any help on this problem.
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