Topic Options
#35024 - 05/28/15 08:25 AM periodic boundary condition centering
Aniko Labas Offline
Forum Member

Registered: 04/15/14
Posts: 25
Dear Users,

I have heme, sodium-ion and NO molecules containing protein solvated with water molecules. The shape of my system is cubic. I would like to set up PBC using the following commands:

! Setup PBC (Periodic Boundary Condition)

stream @mappa/waterbox.prm


open read unit 10 card name @mappa/crystal_image.str
CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma

!Image centering by residue
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname TIP3 end

The waterbox.str file contains:
SET A = 68.2827
SET B = 68.2827
SET C = 68.2827
SET ALPHA = 90.0
SET BETA = 90.0
SET GAMMA = 90.0
SET XCEN = 34.175
SET YCEN = 34.032
SET ZCEN = 34.190

The values A,B and C derive from the end of the previous MD simulation. The central values (XCEN, YCEN, ZCEN) are refers to the geometric center of the protein. (If I set 0 for central values the solvent molecules moves away around the protein, that is why I decided to use these coordinates). The problem is when I run a minimization and after a dynamics simulation the solute and the solvent move away from each other.

Do You have any suggestion why this happens?

Thank You in advance!


p.s.: If I try "coor orient" command before PBC setup the shape of the water molecules distorted.

Edited by Aniko Labas (05/28/15 10:05 AM)

#35025 - 05/28/15 11:57 AM Re: periodic boundary condition centering [Re: Aniko Labas]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8419
Loc: 39 03 48 N, 77 06 54 W
In most case, COOR CONVERT is not needed, unless you are working with crystallographic coordinates.

COOR ORIENT NOROT will translate the box w/o rotation to center it at the origin. The Cartesian origin (0,0,0) is generally recommended for image centering.

The protein is free to move, and is also not subject to image centering; you have also not included the NO molecules or any ions in the image centering, either. This will not go well.

BTW, this post has nothing to do with anything in the Script Archive forum; please choose a more appropriate forum for future posts.
Rick Venable
computational chemist


Moderator:  chmgr, John Legato, petrella