VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 14 2008 - 16:34:22 CST

Hi Tom,
  Adding to what Olaf already indicated, we do have a new 'pbcwithin'
atom selection command in the test versions of VMD 1.8.7 if you would
like to try it out. More work is needed before the PBC display functionality
is as flexible as we'd like however.

Cheers,
  John

On Thu, Feb 14, 2008 at 02:15:15PM -0600, Thomas C. Bishop wrote:
> 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
>
>
>
> --
> ***********************
> * Thomas C. Bishop *
> *Office: 504-862-3370 *
> *CCS: 504-862-8391 *
> *Fax: 504-862-8392 *
> ***********************

Content-Description: Forwarded message - Re: namd-l: NAMD 2.6 dcd and breaking XPLOR
> Date: Thu, 14 Feb 2008 07:14:02 -0600
> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> To: Neema Salimi <nsalimi_at_msg.ucsf.edu>
> CC: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: NAMD 2.6 dcd and breaking XPLOR
>
> 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
> >
> >
> >
> >
> 

-- 
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