VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Thu Feb 14 2008 - 14:15:15 CST

Dear vmd,
the attached NAMD question brings a few VMD questions to mind.

1) do the periodic images displayed with (graphics reps -> periodic ->
+x ; -x etc....) get the PBD dimensions updated every step when
displaying an animation of the trajectory?

2) it seems that atom selections such as
water and within 10 of solute
do not span across periodic boundaries
(in the above I assume that the solute is less than 10 from "wall" so
that the solute actually sees waters on other side of periodic box.
NAMD would see such waters but VMD does not select these, correct me if
I'm wrong please.)

Since there is an exwithin command... how about a pbcwithin command?

3) is there a way to easily display the periodic box size
e.g. a "show pbcbox" or "get pbc dimensions" command or some other way
to obtain values for the PBC dimensions within VMD if it has read them
from the DCD

Thanks in advance for any info.
TOm 

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attached mail follows:

I can verify that aside from the change in header, the 2.6 dcds actually
are storing unit cell information throughout the simulation, which is
useful for a number of reasons (most notably, it allows you to properly
postprocess a trajectory with pressure control, without digging into the
xst). I'm not familiar enough with xplor to know whether it isn't
compatible with dcds that have this information, or if there's some
option that needs to be turned on to allow it to read them. This is,
however, why just modifying the header isn't helping.
Catdcd may help both because it lets you extract pdb frames from dcds,
and may be able to write a different trajectory format that xplor
understands if you need to do something else in xplor. Jim may have
further input; I don't know the dcd format, so I can't comment on the
exact details of what program supports what features.

Best,
Peter

Neema Salimi wrote:
> Using wordom (http://www.biochem-caflisch.unizh.ch/wordom/) to read
> the DCD headers, I have discovered that NAMD 2.6 headers are different
> from 2.5 headers using the same input files. The 2.5 DCDs invariably
> have the "Variable PBC" line set to "0", while the 2.6 DCDs have the
> same line set to "1". Unfortunately, using wordom to modify the DCD
> header doesn't solve the problem. I can use wordom to process the DCD
> files, so I know they're not completely screwed up. Does ANYONE have
> any insight?
>
>
> On Feb 7, 2008, at 3:15 PM, Neema Salimi wrote:
>
>> Did NAMD 2.6 break dcd files for reading into XPLOR? I use XPLOR to
>> do a few things, like extract PDBs from NAMD's binary dcd files. I
>> recently switched to 2.6, and now XPLOR complains that there's no
>> coordinate sets inside the dcd file. My guess is that is has
>> something to how the frames are indexed, but I haven't been able to
>> work it out just yet. And yes, my simulations are running fine, I
>> can convert binary coordinate restart files and the energy outputs
>> look normal. Thanks.
>>
>> Neema Salimi
>> nsalimi_at_msg.ucsf.edu <mailto:nsalimi_at_msg.ucsf.edu>
>>
>> University of California-San Francisco
>> Graduate Group in Biophysics
>> Agard Lab
>> http://msg.ucsf.edu/agard/
>> Lab Phone: (415) 476-5143
>>
>>
>>
>>
>
> Neema Salimi
> nsalimi_at_msg.ucsf.edu <mailto:nsalimi_at_msg.ucsf.edu>
>
> University of California-San Francisco
> Graduate Group in Biophysics
> Agard Lab
> http://msg.ucsf.edu/agard/
> Lab Phone: (415) 476-5143
>
>
>
>