problem w/ free energy perturbation

Date: Wed Nov 29 2006 - 18:51:17 CST

I am a novice to the free energy perturbation method. I have a system in which I gradually turn off the charges of a particular
residue. I get the following error message:

ERROR: Margin is too small for 252 atoms during timestep 1.
ERROR: Incorrect nonbonded forces and energies may be calculated!

It seems like this may be due to the presence of nonbonded interactions between the 'wild type' atoms and the 'mutant' atoms.
(The vdW energy was unrealistically large:99999999.9999.) However, this should not be happening, because I ran the alchemify
program, which is supposed to specify the exclusions.
Thanks in advance!

Omar Demerdash

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