RE: PBC error. Amber force field in NAMD

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Sep 25 2018 - 11:35:42 CDT

Rectangular boxes are pretty straightforward. Only three of the basis vector elements will be nonzero, with the nonzero elements dictated by how large the initial size of the box is along that axis. Your cellOrigin is more or less arbitrary if you don't turn on wrapping for your protein component (wrapAll off), and can safely be set to 0 0 0.

So you'd want something like this:

cellBasisVector1 x 0 0
cellBasisVector1 0 y 0
cellBasisVector1 0 0 z
cellOrigin 0 0 0

For hexagonal boxes or triclinic cells, the other values become relevant.

-Josh

On 2018-09-25 05:47:14-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Dear NAMD users,
I want to use amber force field in NAMD. I have prepared the topology (.prmtop) and coordinate (.inpcrd) files in tleap. I want to use this topology in NAMD. HOW I can set Periodic cell vectors in .namd configuration file.
while setting COM of protein as cell origin the box breaks in minimization.
Mine is a rectangular box with protein on one corner(for SMD constant velocity pulling).
I want to set the following values in namd configuration file.
cellBasisVector1 x1 y1 z1,
cellBasisVector1 x2 y2 z2,
cellBasisVector1 x3 y3 z3
cellOrigin x y z
And the information I have
from .prmtop file
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
  9.00000000E+01 8.85883700E+01 8.84811760E+01 2.08344945E+02
 and from leap.log file
Box:
   enclosing: -45.96 -33.88 -96.75 43.62 36.38 -25.03
   sized: 82.04 94.12 31.25
   edge: 128.00
Resolution: 1.00 Angstrom.
>From this information how i can get information for using in .namd configuration file?

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