From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Thu Jun 24 2010 - 16:03:15 CDT
I am using NAMD to get the PMF profile for an ion transport process.
When using the "Periodic Boundary Conditions" and the "PME" in configuration file for "minimization and equilibration in the water box", everything is fine and the XSC files (extended system files) are all produced. But, using the same parameters for an ABF calculation on the same system, NAMD is hanging at the start of the job and no XSC file is produced and I get the error below:
OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: Bad global exclusion count!
Looking at NAMD mailing list it seems that if the periodic box size is smaller than the system size or if The PMF grid size is smaller than periodic size or if the cutoff and switchdistt are too small this can cause the above error. My question is that if any of these cases can cause such an error shouldn't this happen in minimization and equilibration calculation as well? Does anyone know another source of problems?
Thanks for your time,
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