[gmx-users] rvdw, rlist and rcoulomb for Amber03
rajatdesikan at gmail.com
Sun Aug 25 06:01:53 CEST 2013
In a recent post
you commented that:
"Unless you can demonstrate that your changes in cutoffs do not produce
artifacts or lead to other inaccuracies using robust test systems, I
wouldn't recommend any deviations."
I have the habit of reading the original forcefield papers and using their
parameters directly. In this regard, I use rlist=rvdw=rcoulomb=0.8 nm for
Amber03 (same parameters are used in the following tutorial:
My system is a protein in a water box with counter-ions and 0.1M NaCl. It is
a NVT simulation at 310 K.
My queries are the following
1) Are my parameters appropriate for Amber03?
2) How would I go about constructing robust test systems to demonstrate the
validity of my parameters for a protein in a water box? What parameters do I
measure? Energies? Any structural parameters in particular?
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