From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Apr 04 2013 - 09:56:46 CDT
Make sure that you used the same type of switching function in both programs (option vdwForceSwitching in NAMD).
----- Original Message -----
> We performed MD simulation using NAMD program and used charmm force
> field. During the MD the non-bonded interactions were set to switch
> between 10A to 12A distance and pair list were truncated at 13.5A.
> Later the trajectory is analyzed and as a benchmark we are trying to
> reproduce the bonded and non-bonded energies using CHARMM package’s
> analysis tools. The values of the bonded terms are accurately
> reproduced in CHARMM, i.e. energies in the NAMD output file match
> with CHARMM. But we are unable to reproduce the van der Waals term.
> In CHARMM in put script we have set CTONNB 10, CTOFNB 12 and CUTNB
> 13.5, i.e. exactly the same condition of NAMD input. But the numbers
> from two calculations are not matching. They differ by
> ~60-100kcal/mol. Can anyone suggest any point that we might be
> missing which could be the reason of this mismatch?!!
> Shubhra Ghosh Dastidar
> Kolkata, India
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