[gmx-users] free energy: annihilation

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 26 10:16:01 CEST 2006


I'm trying to annihilate a complete DMSO box at constant volume. The 
dG/dlam values converge nicely but when I integrate the curve I get a 
Helmholtz energy that is almost exactly a factor of two different from 
the experimental value.

Am I forgetting something here? Should I treat the intramolecular 
degrees of freedom in a special manner? Currently I am only turning off 
the LJ and Coulomb terms. Should I turn off the angles and dihedrals as 
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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