[gmx-users] solvation free energie calculations

Tivadar Orban t.orban at csuohio.edu
Wed May 5 22:18:00 CEST 2004

On 5/5/04 12:49 PM, "Craig Swank" <craigswank at hotmail.com> wrote:

> 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:
> http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html
> 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.
> Craig
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