AMBER Archive (2008)

Subject: AMBER: Gradual releasing of position restraints

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Tue Nov 25 2008 - 08:23:02 CST

Hello, my question is about equilibration of two chain protein at constant
pressure.
After energy minimization and gradual heating at constant volume I switch to
constant pressure simulation. And during 50ps density equilibration with 2.0
kcal/mol-A2 position restraints on protein,
structure of my protein seems to become compressed. This appears because
of my protein consists of two chains that become
closer to each other during box size decrease. After density equilibration I
release restraints completely
and strained interchain conformation leds to unfavorable large
fluctuations in protein.
So I suppose that problem could be partially resolved by gradual releasing
of position restraints.
I want to release restraints in several steps, for example:
step1: 50ps, 2.0 kcal/mol-A2 position restraints on protein.
step2: 50ps, 0.5 kcal/mol-A2 position restraints on protein.
 step3: 50ps, 0.1 kcal/mol-A2 position restraints on protein.
step4: equilibration without restraints.

Could you advise me rational restraint values for each step? I know that 2.0
kcal/mol-A2 restraint rather strongly fix atoms at initial position
so I suppose this value is appropriate for first step. But what restraints
is appropriate for other steps?

Dmitri Nilov,
Lomonosov Moscow State University

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