VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 01 2009 - 10:07:57 CST

Hi,
  You can compute the three basis vectors from the alpha/beta/gamma/a/b/c
values in the DCD file, but this will only work if you happened to have
basis vectors that are directly representable in the crystallographic
angles/lengths convention. If your system is rotated, then this won't work.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 30, 2009 at 03:49:43PM +0530, Neelanjana Sengupta wrote:
> Hi VMD users,
>
> I had to kill a NAMD simulation before completion as our cluster had to be
> shut down. My restart frequency being 1, I could restart later from the
> end point with the restart.vel, restart.coor and restart.xsc files.
> However, the .xsc file for the full trajectory (as much as it could run)
> is not written down.
>
> Now, I am interested in running NAMDenergy, and do need the .xsc file for
> calculating some energies for my periodic system. The GUI version allows
> one to write an .xsc if one is not available. Is there a way to do this in
> the command line version of NAMDenergy (or maybe a more general way of
> writing it, without even resorting to NAMDenergy)?
>
> Also, I guess NAMDenergy writes the .xsc using the cell information at
> each step in the .dcd (assuming the .dcd contained the unit cell
> information). Please correct me if I am wrong here...
>
> Thanks!
> -Neela 

-- 
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