Alchemical Free Energy Perturbation Simulation

From: Jawahar Neelankatan (
Date: Fri Jul 28 2006 - 11:18:20 CDT

Hi all,
I am doing an Alchemical FEP simulation involving the alchemical transformation of one ion to another inside a polar solvent. I initially did these simulations with OPLS parameters and I got correct results.
  I am now trying to repeat this exact simulation using CHARMM parameters but I am getting a really strange error. The FEP simulation runs for a while, then at some point, it crashes with the error:

FATAL ERROR: Error on renaming file fepch.xsc to fepch.restart.xsc.old. No such file or directory

This error occurs at random points in the simulation when an attempt is made by the program to write the extended system to restart file. This is a really weird error because the program runs fine at first, and is able to write the extended system (.xsc) and the restart file (.restart.xsc.old). It does this for several steps, with no hitches whatsoever, and then it suddenly gives this error about not being able to find the .xsc file. This is quite bizarre because, during the last run, I took specific care to make sure that both the .xsc and .restart.xsc.old files were present while the simulation was running. Everything seems to go smoothly until the .xsc file somehow disappears and the program flags this error when it doesn't find it. I'm totally stumped because when I run the exact same Alchemical FEP simulation using OPLS parameters (instead of CHARMM parameters), the program works fine. Any ideas as to why this is happening ? I have tried to run this simulation several
 times, but each time it gives the error about not finding the .xsc file, and when I check the directory, the .xsc file that I previously observed has disappeared. Is NAMD deleting it ? If so, why ?


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