Re: Constant pressure MD problems (sander)

From: David A. Case <>
Date: Mon 12 Aug 2002 08:47:10 -0700

On Mon, Aug 12, 2002, Pratul Agarwal wrote:
> After I have solvated the protein complex (tLeap), I have performed
> minimization of the protein only and then water only. The next step I
> want to perform is to remove the "bubbles" and get the system to a
> reasonable density. For this, I plan to do a 25 ps (25000 steps in 1 fs
> steps) simulation at constant pressure (NTP=1) with a coupling to bath
> (NTT=1). I found that my job was bombing out with an a short error
> message:
> --
> EWALD BOMB in subroutine ewald_list
> volume of ucell too big!!

First, be sure that the temperature is equilbrated *first* to around 300k
at constant volume, before turning on constant pressure. Although you
don't explicitly say, it may be(?) that you are trying to adjust the box
size before you have a well-equilibrated system at a reasonable temperature.
The constant-pressure algorithm is not smart enough to handle this.

Second, don't let taup get too small .. a value of 1 ps should be plenty
short. This will keep the volume from (over)-adjusting too rapidly.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Aug 12 2002 - 08:47:10 PDT
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