AMBER Archive (2008)

Subject: AMBER: Thermodynamic integration with positional restraint?

From: Cen Gao (
Date: Thu Jan 03 2008 - 10:43:32 CST

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

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