Re: PME box ?

From: David Smith <>
Date: Wed 05 Jun 2002 16:15:44 +0200

Yi ming Cheng wrote:
> Dear Amber users:
> Would you please to tell me about the meaning of the sentence below which
> appears in the tutorial? Or tell me
> how to do this. THANKS.
> "PME box size information must be updated to match the final box size from
> the previous run."
> Tutorial:
> DNA --> Equilibrating and running the poly(A)-poly(T) structure -->
> Step 3: Moving the DNA

I'm still using Amber 6 so if the following is out of date, please
accept my apologies.

If you are using periodic boundary conditions the Particle Mesh Ewald
(PME) code needs to know how big your box is. This information is stored
in your prmtop file and if it is your first run with this file then the
program will take it from there. If you haven't ever changed to volume
of your box by (for example) running with constant pressure then you
don't have to worry about it. If, however, the volume (and therefore the
dimensions) of your box has changed, you have to take a little care
about where the program is getting the box dimensions from.

If you are restarting an MD run and you wish to use the final velocities
from the previous run as the initial velocities for the new run you can
set NTX=7 and the program will read the coordinates, velocities, AND box
size from the restart file.

If, after a constant pressure run in which the volume has changed, you
wish to start a minimization or an MD run NOT using the final velocities
you need to tell the ewald code the new dimensions of your box
explicitly. You can find the new dimensions in the very last line of
your restart file. The first three numbers are the box dimensions and
the last three the angles that define your box geometry (90.0 if you are
using a rectangular box).

e.g. if you found:

 111.4266801 86.0258059 93.6675901 90.0000000 90.0000000 90.0000000

You would add:

  A=111.4266801, B=86.0258059, C=93.6675901,

To your mdin file just after the &cntrl &end namelist.

Hope this helps.

Good luck.
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Tel.: +49 (0)89 2180 7740
Fax.: +49 (0)89 2180 7738
Received on Wed Jun 05 2002 - 07:15:44 PDT
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