I use Amber6 too. In Amber 6, you do not need to bother to set the A, B, C
parameters of PME box in the input file, even if ntx=1 instead of 7.
Sander is smart enough to use the readin periodic box size (from the last
line of the input coordinte file) as the PME box size. Although this is
not indicated in the manual, it is true.
Hai
On Wed, 5 Jun 2002, David Smith wrote:
> 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 I'm still using Amber 6 so if the following is out of date, please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:
>
> &ewald
> A=111.4266801, B=86.0258059, C=93.6675901,
> &end
>
> 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
> Germany
> Tel.: +49 (0)89 2180 7740
> Fax.: +49 (0)89 2180 7738
> e-mail: David.Smith_at_cup.uni-muenchen.de
> ---------------------------------------
>
>
Received on Wed Jun 05 2002 - 09:07:29 PDT
