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: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Aug 12 2002 - 08:47:10 PDT
