Hi,
> But when the output file is generated by sander, in the section that says
> Free energy parameters, I dont see dvdl_norest being printed at all.
This print statement seems to be missing. The option should nevertheless
be set correctly...
> The input file for the V0 state:
> ifsc=1, dvdl_norest = 1,
> The mdin file for production run for state V1:
> ifsc=1, dvdl_norest = 1,
hm, this will not work. The manual should be clearer on that, but
dvdl_norest is set up to work for restraints on the disappearing side
only, not the appearing. This is because it is used for absolute binding
free energies. It never occured to me that someone would like to remove
and introduce restraint particles at the same time.
However, you can just not use dvdl_norest and subtract the restraint
contribution by hand.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jan 26 2012 - 08:00:02 PST
