Re:Alchemical Free Energy Perturbation Simulation

From: yi wang (
Date: Wed Aug 02 2006 - 12:10:51 CDT

Hi Jawahar,
      It is indeed a very weird error message you have there. The only
thing that looks a bit abnormal to me is that NAMD is trying to rename
*.xsc file to *.restart.xsc.old file. Because the *.xsc file usually
shouldn't be written until the very end of the simulation when NAMD
finishes. During the run, you should only have .restart.xsc file and
the .restart.xsc.old file, which is the case with me when I run FEP
using NAMD. (Of course this is assuming that your naming of the files
is the same with what's suggested in the tutorial).
     I would disable FEP and run a pure equilibration first using CHARMM
parameters and see if everything looks right. Please let us know if the
problem stays.
Good day!

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