From: Jennie Thomas (
Date: Tue Jun 19 2007 - 18:28:12 CDT

Hi John,

Thanks for your fast response. I have uploaded one case to the
following folder:


under the VMD Public filesystem. I also uploaded a short .tcl script
that should just read the trajectory and then print out the box
dimension for each step. I've uploaded both the pdb and CHARMM
coordinate files, but it doesn't matter which I use. These
simulations were run by the MacKerell group, I asked them to check
these are really constant pressure. They confirmed that the box
information is there and also confirmed these are really constant

Thanks for your help with this.

On Jun 19, 2007, at 4:03 PM, John Stone wrote:

> Hi,
> I would expect this to work correctly, but it's possible that
> you have an error in your analysis script, or that the CHARMM
> trajectory doesn't actually contain PBC cell information for
> some reason. Please post the test case you're looking at into the
> VMD Public project BioFS area and I'll look at it closely (see
> instructions on joining the VMD project below):
> Cheers,
> John Stone
> On Tue, Jun 19, 2007 at 03:59:53PM -0700, Jennie Thomas wrote:
>> Hello,
>> I'm loading a CHARMM coordinate file and then a CHARMM trajectory
>> into vmd from an NPT simulation. However, vmd isn't reading the box
>> dimensions from the trajectory (even though we've checked to make
>> sure they are there).
>> I'm using the following version of vmd:
>> 1.8.6 MacOS X OpenGL Intel 86 (Apple MacOS-X (10.4.7 or later) with
>> hardware OpenGL (native bundle))
>> Any ideas on why the box information isn't available at each step?
>> If needed I can post a sample trajectory, coordinate file, and tcl
>> script that reads the trajectory and prints out the x box dimension
>> at each step (right now this is the same at each step, but it should
>> be fluctuating).
>> With thanks,
>> Jennie Thomas
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