AMBER Archive (2008)

Subject: Re: AMBER: Thermodynamic integration with positional restraint?

From: David A. Case (
Date: Thu Jan 03 2008 - 11:31:19 CST

On Thu, Jan 03, 2008, Cen Gao wrote:
> 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?

You can have a different value of NTR in the two groups: this is effectively a
part of the energy model, which is supposed to be different at the two
endpoints. Other things that just involve the force field (e.g. the cutoff,
scnb, etc.) can also differ.

The parts that must be the same involve anything relating to the way in which
the MD integration is done: shake, time steps, temperature and pressure
regulation, etc.

We need to update the manual to make this point clearer.

...hope this helps...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to