VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 15 2009 - 14:32:57 CDT

Hi,
  Hopefully Olaf Lenz (main pbctools author) can address your question,
but he may need to have a copy of the particular structure/trajectory/xst
files you're using in order to figure out what is going on.
If you can post them on the web somewhere where he can download
them, I'm sure it'll make it easier for him to investigate.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Wed, Jul 15, 2009 at 11:05:01AM +0100, Patrick Kiley wrote:
> Dear all,
>
> I have run a simulation using namd with non-orthorhombic periodic boundary
> conditions and would like to check the periodic box of the simulation
> before I continue with my work. To do this I am using the VMD1.8.7b5 plugin
> pbctools:
> >Main< (xyz) 43 % pbc box -center com
>
> The problem I have is that the box I see is wrong (see attached)- it is not
> the box in my .conf file, .xst file, or the box in the beginning of my namd
> log file. All three of these agree. See below.
>
> >From .log file :
> Info: PERIODIC CELL BASIS 1 45.288 0 -6.89027
> Info: PERIODIC CELL BASIS 2 0 60.678 0
> Info: PERIODIC CELL BASIS 3 -0 4.7 88.18
>
> >From .conf file :
> cellBasisVector1 45.28800010681152 0.000000 -6.890269
> cellBasisVector2 0.000000 60.67799949645996 0.000000
> cellBasisVector3 -0.000000 4.700000 88.18000030517578
> cellOrigin 0 0 0
>
> >From end of.xst file :
> (omitted 297 lines . . . all exactly the same)
> 298 45.288 0 -6.89027 0 60.678 0 -0 4.7 88.18 0 0 0
> 299 45.288 0 -6.89027 0 60.678 0 -0 4.7 88.18 0 0 0
> 300 45.288 0 -6.89027 0 60.678 0 -0 4.7 88.18 0 0 0
>
> However, when I run this command:
>
> >Main< (xyz) 44 % pbc get -namd
>
> I get this output: {{45.809155 0.0 0.0} {1.08910732527e-07 60.678001 0.0}
> {-13.2633705032 4.69999725436 87.176807261}}
>
> Which doesn't agree with the other three files. In particular X3 and Z1 are
> totally different from what they should be.
>
> I couldn't find a similar problem anywhere in the docs/internet, so here
> are my questions: A) which is correct - I am inclined to believe what I see
> more than what I read, but then why is the .xst file in disagreement? B)
> from the documentation, pbctools seems to like alignment with the X axis
> (-alignx vs -noalignx)- does this mean that any box that isn't aligned with
> the X axis will be displayed incorrectly? C) How can I verify which is
> correct/make sure my simulation has the correct box/see that box properly
> displayed?
>
> Thanks very much for your time, (also, I apologise in advance if this is
> namd-l question, but VMD-l seems more appropriate)
>
> Patrick Kiley
>
>
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078