[gmx-users] rvdw, rlist and rcoulomb for Amber03

[Rajat Desikan]

Hi Justin,
In a recent post
(http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944)
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:
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) 
).

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?

Thank you.



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