VMD-L Mailing List

From: Ana Celia Vila Verde (avilaverde_at_fisica.uminho.pt)
Date: Thu Feb 02 2006 - 08:32:35 CST

John Stone and Joshua Moore: thank you for replying so rapidly and with such
detail. It was very, very helpful for me.

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
_________________________________

-----Original Message-----
From: Joshua D. Moore [mailto:jdmoore_at_unity.ncsu.edu]
Sent: Wednesday, February 01, 2006 7:27 PM
To: Ana Celia Vila Verde
Subject: Re: vmd-l: a question about dcd files

Hi Ana,

Yes John is right as you are.

However, minimization steps are written to the dcd file. So if you start
at time 0 and minimize for 5000 steps, and you write the dcd file every
250 steps, the first dcd frame will be at step 250. The xst file,
however, (if you are running NPT) is not written until the minimization is
over because the minimization is at constant volume so there is no need to
store this information over and over again.

The starting conditions (starting from time 0 or whatever your starting
time is) are never written to the dcd file. Like John said, if you want
this you should load your .pdb. For restarts, you will have the starting
frame as the previous run's last frame, so there is not a need to write
the starting conditions.

Josh

On Wed, February 1, 2006 2:53 pm, 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
>
> _________________________________
>
>
>
>
>
>
>
>
>
>

--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------