VDW component: NAMD vs. CHARMM

From: Shubhra Ghosh Dastidar (sgducd_at_gmail.com)
Date: Thu Apr 04 2013 - 09:20:23 CDT

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 packages 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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