VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2006 - 14:29:15 CST

Ana,
  My understanding is that the first saved DCD frame in a NAMD job will
NOT be the intial conditions, but rather the "Nth" simulation timestep
if you're saving DCD frames every N timesteps. So you should not expect
to get exactly the same results from Stride on the secondary structure etc
unless very little has changed from the initial conditions. If you want the
initial conditions to be the first frame loaded in VMD, you can simply
load the PDB you started with before loading the subsequent DCD file(s)...

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 01, 2006 at 02:53:39PM -0500, Ana Celia Vila Verde wrote:
> Hi,
>
>
>
> I noticed when I load a pdb and a psf file of a molecule with helices into
> VMD, and then type on the TK console
>
>
>
> set getHelix [atomselect top "helix and name CA"]
>
>
>
> I select all the alpha carbons involved in the helices.
>
>
>
>
>
>
>
> However, if I run a simulation with that molecule in NAMD, load the pdb, psf
> and dcd files into VMD and then type on the TK console
>
>
>
> set getHelix [atomselect top "helix and name CA" frame 0],
>
>
>
> I get a different selection.
>
>
>
>
>
> I checked the literature and found that the initial positions (I’m assuming
> that this means the coordinates found in the PDB file) are not recorded in
> the DCD file, so I’m guessing that the coordinates stored in frame 0
> correspond to the coordinates of the molecule after minimization and before
> the actual run starts. Could someone confirm this?
>
>
>
> Thanks,
>
>
>
> Ana
>
>
>
> _________________________________
>
> Ana Célia Araújo Vila Verde
>
> Penn State University
>
> Department of Chemical Engineering
>
> Fenske Laboratory
> University Park, PA 16802
>
> USA
>
>
>
> Phone: +(1) (814) 863-2879
> Fax: +(1) (814) 865-7846
>
> avilaverde_at_engr.psu.edu
>
> _________________________________
>
>
>
>
>
>
>
>
> 

-- 
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