AMBER Archive (2002)

Subject: INTPRT and PMF

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Tue Apr 23 2002 - 13:23:36 CDT

Hello,

I have a question regarding the INTPRT flag. Normally, when doing FEP, should
the INTPRT be set to something other than zero in order to calculate the
intra-perturbed group contributions? From reading the J.Chem.Phys.94(6)paper
(The overlooked bond-stretching contribution in free energy perturbation
calculations), where PMF calculations together with SHAKE were used to
calculate these intra-perturbed group contributions, it seems to me that these
contributions should always be calculated and therefore when performing FEP,
using SHAKE and setting NCORC = 1 (PMF on) would include these contibutions.

What sort of calculations occur when INTPRT is set to something other than
zero while the PMF is turned off? Are the intra-perturbed group contributions
still being calculated? When should PMF be turned on and what should INTPRT be
set while doing free energy calculations. I did read the manual and the paper
that I have mentioned but I would still appreciate some information on these
topics.

Thanks in advance

Sophia Kondratova
Chemistry Graduate Student
University of New Brunswick
Fredericton, Canada