[AMBER] NPT and restraints

From: Dmitry Mukha <dvmukha.gmail.com>
Date: Sun, 30 Jan 2011 17:13:22 +0200

Dear Amber users,

is there any opportunity to run MD of NPT ensemble with harmonic restraints?
I have tested many combinations of taup, vrand (ntt=2), gamma_ln(ntt=3),
restraints_wt, and all that I've got are systems with density equal or below
starting value. Generally, systems blow up due to the energy, I guess,
introduced by barostat action on restrained atoms. These atoms work as
springs releasing additional potential energy after coordinate scaling.
Temperature raises continually, and barostat scales coordinates in order to
enlarge system's volume and, thus, compensate growing pressure. If dt is
small enough, this process can be computed till almost stable state with
density significantly below initial. Final density values depend on
termostat coupling tightness. With tight coupling (low vrand or high
gamma_ln) systems do not evolve and density remains almost the same as
initial. How to overcome these problems and equilibrate density with
restraints applied to solute atoms?

Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Sun Jan 30 2011 - 07:30:02 PST
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