[gmx-users] solvation free energie calculations

Craig Swank 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.

Is your PC infected? Get a FREE online computer virus scan from McAfee® 
Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963

More information about the gromacs.org_gmx-users mailing list