VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Mar 12 2015 - 02:27:03 CDT

If you wrapped using f.i. “-center com” you need to use the same parameters for “pbc box”.

Example:

 

pbc box -center com -centersel protein

 

or what usually works out fine:

 

pbc box -center bb -centersel all

 

Norman Geist.

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Josh Vermaas
Sent: Wednesday, March 11, 2015 5:08 PM
To: Kevin C Chan; VMD Mailing List
Subject: Re: vmd-l: PBC Plugin

 

Hi Kevin,

Does "pbc get" give you what you expect? I suspect what is happening is that it is drawing a box of the correct size, but at the wrong origin. I don't typically draw the boxes, so someone else may have more info, but I suspect if you recentered the trajectory so that it is centered on the origin, the box will encompass your trajectory.

-Josh Vermaas

On 03/11/2015 10:09 AM, Kevin C Chan wrote:

Dear Users,

 

I am currently confused by the pbc plugin shipped with VMD 1.9.2. I have executed the following steps:

 

mol new ionized.psf

mol addfile npt-1.dcd

 

pbc readxst npt-1.xst

pbc box

 

However, on the OpenGL display, it gives a box besides my system. I have checked my PBC parameters by drawing a sphere at the box centre manually read from the xst file and it is lying at the centre of my system. I have no idea what could be possibly wrong to cause a box appearing at another unexpected position (few nm away).

 

Thanks in advance,

 

Kevin
PhD Candidate
Department of Physics and Material Science
City University of Hong Kong
ukevi_at_gmx.hk