Just a proposal.
I think it makes sense to fix the 1-4 scaling factors and put them with
the parm.dat file. I believe the reason they were "tunable" really because
earlier need to accommodate different types of scaling factors and the
desire to have unified torsion parameters. Because torsion parameters have
been tuned with a set of 1-4 scaling factors, changing these factors can
mess up the torsion balance of the entire force field. Yet, it is
attempting to "try it out" when it is part of the input parameters. But
for non-specialists, who might have become the main user group of
AMBER, this all sounds really confusing. So, logically, they should be in
the parm/topology parameter file and should not be allowed to change
during a run.
yong
Received on Wed Apr 05 2006 - 23:49:57 PDT
