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From: Rebecca Perlow <rp284_at_SCIRES.ACF.NYU.EDU>
Date: Thu 22 Jul 1999 16:01:01 -0400

Dear AMBER users,

I am equilibrating a large system with a periodic box and neutralizing sodium ions. During the equilibration, I have frozen the protein using the ntr option.
I adjusted the density of the system by running constant volume MD and decreasing the size of the periodic box gradually. However, upon achieving a density of 1 and switching to constant pressure for the remainder or the simulation, I encounter two problems.
1. As the constant pressure MD proceeds, the pressure remains fairly constant, but the density of the system is steadily decreasing, reaching ~.96 by 4 ps. Is there something I can do to prevent this and keep the density more stable and closer to 1 at constant pressure, or is this normal?
2. The system encounters a fatal error involving SHAKE after 4.06 ps stating that coordinate resetting cannot be accomplished, deviation is too large.
NITER, NIT, LL, I, and J are : 0 2 29 49 50
However, UNLIKE the question in the commonly asked questions section of the AMBER web page, I have IFTRES=1 already since my system is very large.
SHould I continue the equilibration at constant volume or is there some way around this error with constant pressure? I'm using 9A for the nonbonded cuttoff (with PME), should I increase this value?

Thanks so much for your advice on this matter.

-Rebecca Perlow

Rebecca Perlow
Department of Biology
New York University
100 Washington Square East
New York, NY 10003
Tel: (212)998-8228
E-mail: perlow_at_alum.mit.edu
Received on Thu Jul 22 1999 - 13:01:01 PDT
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