Hi,
> A new question arises then: can I apply the restraint only to the
> benze state? As I specify restraints on the benzene molecule in the
> DISANG file it will not make sense to apply this same restraints to a
> system without benzene.
Yes, restraints can differ between systems (or be applied for only one
system), for precisely that reason. You can set dvdl_norest=1 if you want
sander to automatically subtract the restraint contributions from dvdl,
where they should not be counted.
A note of caution: This feature hasnt been used very much so far and it
assumes that V0 is the state with restraints and V1 the state without. It
*should* work the other way round as well, but you are very much
beta-testing here, look at your outputs with care.
Also, you will have to do several additional calculations about adding the
restraints, removing the charges first, reappearing the molecule in water
and apply an analytical correction for the restraints. You probably know
all that from the literature, I wanted just to point out that the result
from this one TI calculation will have no connection to experiment on its
own.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jan 13 2010 - 05:00:03 PST
