Dear Amber Users:
We are trying to calculate the free energy difference between two
molecules, say, molecule A and B. But we want to add several
positional restraints to molecule B only.
My question is can we perform Thermodynamic integration with those
positional restraints only turned on in molecule B. That is, set NTR=1
and use a refc file only for molecule B. According to the manual p153,
"the input (mdin) file must be the same for the twogroups", which
means I cannot set NTR=1 only for one group. Is there any way I can
get around with that?
Thanks & Happy New year
Cen
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Jan 05 2008 - 00:03:30 PST
