[gmx-users] solvation free energie calculations
t.orban at csuohio.edu
Wed May 5 22:22:00 CEST 2004
On 5/5/04 12:49 PM, "Craig Swank" <craigswank at hotmail.com> wrote:
I tried out recently the FEP tutorial that you are talking about, and I had
no problem with it (i.e., I've got pretty much the same values for dgdl as
in the example. What version are you using?
> 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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