VMD-L Mailing List

From: Patrick Kiley (pjk38_at_cam.ac.uk)
Date: Wed Jul 15 2009 - 05:05:01 CDT

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


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