VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 12 2009 - 20:25:30 CST

On Thu, Nov 12, 2009 at 8:40 PM, A D <boltzmanndist_at_yahoo.com> wrote:
>
> Dear VMD Users,
>
> I am using the PBCTools plug-in to find the unitcell parameters of my hydrated membrane system. Here is the code I am using:

> ##############################
> set mol0 [mol new system.psf type psf waitfor all]
> mol addfile system.pdb type pdb waitfor all molid $mol0

why not read the CRYST1 record from the .pdb file?

> set cell [pbc get -vmd -now -check]
> set file1 [open "cellvectors.dat" "w"]
> puts -nonewline $file1 $cell
> ##############################

> The code "works" and gives me a,b,c,alpha,beta and gamma when I use it with the PDB file of the system that I retrieve after several nanoseconds of NAMD simulation. However, when I used the code with the PDB file of the system at 0 nanoseconds, I get all 'zero' unitcell vector lengths, and the "check" functionality of the 'get' command results in the following note: " -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000). Have you forgotten to set the pbc parameters?"
>
> I could not understand this dichotomy. I need valuable comments of someone who is more knowledgable concerning this topic.

the explanation is very simple: VMD can only give you information that
you provide
or information that is derived from what you provide.
obviously one of your .pdb file contains information about the size of
the simulation cell,
the other one doesn't. if it doesn't, pbctools gives you the message
that you report.

the message originates from the fact that pbctools is a combination
(and massive rewrite)
of several pbc handling related scripts and plugins, and one of them
was written to
read in the information of the simulation cell from an .xst file that
NAMD creates during
simulations.

cheers,
   axel.

> Thanks for reading,
>
> Seth. 

--
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.