AMBER Archive (2006)

Subject: AMBER: positional restraints & constant pressure

From: Kateryna Miroshnychenko (
Date: Thu Feb 02 2006 - 09:40:30 CST

Dear all,

I would like to clarify some questions concerning the usage of positional
restrains(ntr=1) with constant pressure(ntb=2, ntp=1).
According to the Amber Manual ntp=1 means isotropic position scaling.
Does this mean that the coordinates of the center of mass of my
molecule will be shifted as a result of pressure scaling?

If so, than how the coordinates of my molecule can be restrained to
the coordinates of the reference structure? Are the centres of masses
of these two molecules superimposed before restraints are applied?

As far as I've understood while reading the answers from the AMBER
mail archive, the usage of ntr=1 with small force constant, less than
5kcal/(molA2), and ntb=2, ntp=1 should not give any problems. Is it
just due to the small value of force constant? Can the usage of ntb=2
with ntr=1 during all the md simulation cause some potential problems?

Any suggestions would be helpful.
With many thanks in advance,


 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine

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