VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 16 2003 - 10:00:27 CDT

Hi,
  I'm forwarding Jan Saam's reply on this since it bounced this morning:

----- Forwarded message from owner-vmd-l_at_ks.uiuc.edu -----
Subject: Re: solute + solvent temperature?
From: Jan Saam <saam_at_charite.de>
Reply-To: saam_at_charite.de
To: vmd-l_at_ks.uiuc.edu

Hi,

you can calculate the temperatures from the simulation restart final
output files (from th *.vel pdb files that store the velocities.)

If you need the temperatures of the entire trajectory yuo must specify
velDCDfile and velDCDfreq in your NAMD config file in order to obtain a
DCD file that contains the atomic velocities (the normal DCD file does
only contain the atomic coordinates).

You can load this velDCD file together with your psf file in VMD. It
looks quite funky, somehow like a sparkling star, but you can do the
same selections as with your coordinate dcd file.

eg.
set sel [atomselect top "water"]
set velocities [$sel get {x y z}]

Hope that helps,

                Jan

Am Fre, 2003-05-16 um 08.04 schrieb Charles McCallum:
> That's just what I was thinking too --- you could run analysis tools on
> the output trajectory files. Use the "select" command in charmm and
> you should be able to do it.
>
> Cheers,
>
> Mike
> On Thursday, May 15, 2003, at 16:00 US/Pacific, Ioana Cozmuta wrote:
>
> > Hi,
> >
> > Just a guess: I think you can calculate that, you have the velocities
> > for each atoms
> > in the trajectory file so with a script you can calculate from the
> > velocities the temperatures, right, separately for the solute and
> > solvent?
> > Just that you need to know the order the atoms are written out in the
> > trajectory file :)
> >
> > Ioana
> >
> > On Thu, 15 May 2003, John Stone wrote:
> >
> >>
> >> Hi,
> >> Neither VMD nor NAMD can do this presently.
> >> I checked with Jim (main NAMD developer) to make sure.
> >>
> >> Thanks,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >> On Wed, May 14, 2003 at 09:55:35PM +0100, Shantenu Jha wrote:
> >>> Can NAMD/VMD be used to determine the solute & solvent temperatures
> >>> separately?
> >>>
> >>> Thanks.
> >>> Shantenu
> >>>
> >>
> >> --
> >> 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
> >>
> >
> >
> --
> C. Michael McCallum
> http://chem.cop.uop.edu/cmmccallum.html
> Associate Professor
> Department of Chemistry, UOP
> mmccallum .at. uop . edu (209) 946-2636 v / (209)
> 946-2607 fax
>

----- End forwarded message ----- 

-- 
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