From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Mar 30 2011 - 09:16:21 CDT

Well yes in the VMD manual.
http://www.ks.uiuc.edu/Research/vmd/current/ug/node135.html

On Wed, Mar 30, 2011 at 15:16, Donovan B.T. <B.T.Donovan_at_soton.ac.uk> wrote:

> Thanks!
>
> I've now engineered a suitable PSF file and now the queries in VMD seem to
> work well for charges and simple dipole measures. I wanted to check about
> the dipole measure implementation. Does it work in Debyes yet? I saw
> something related to that before in a previous post. Is there any more
> documentation anywhere for "measure dipole" with suitable switches?
>
> Best
>
> Brett
>
>
> ________________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Friday, March 25, 2011 2:11 PM
> To: Donovan B.T.
> Cc: Pawe? K?dzierski; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: measure dipole
>
> Hi,
> VMD doesn't compute partial charges, as these are normally
> provided by the force field your simulation is based on, and in most
> cases you would get the charge information into VMD by loading it from
> a file format that includes it. If you were using NAMD/CHARMM, that would
> be from a PSF file. I believe there was a script called "top2psf" for
> Gromacs that generates a PSF file from a .top file. I don't know how
> well it works, but it might give you the charge information that is
> not included in the XTC and GRO files.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 25, 2011 at 01:18:38PM +0000, Donovan B.T. wrote:
> > Hmm, I seem not be pulling out any charge information at all.
> >
> > >> set selatoms [atomselect top "name OW and (resid 129)"]
> > >> $selatoms get charge
> > 0.0
> >
> > This should be a oxygen atom on a water. There seem to be no partial
> charges at all. There are .gro and .xtc files [not my simulations] used to
> create the VMD render . Is VMD not computing the partial charges on the
> atoms??
> >
> > Thanks
> > ________________________________________
> > From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Pawe? K?dzierski [pawel.kedzierski_at_pwr.wroc.pl]
> > Sent: Friday, March 25, 2011 7:55 AM
> > To: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: measure dipole
> >
> > On 24.03.2011 19:07, Donovan B.T. wrote:
> > > Getting measure dipole to work.
> > >
> > > I have a membrane system with water and I want to select a region and
> compute the dipole moment at that region. For a test case I tried just a
> single lipid, where this is selected as follows:
> > >
> > >
> > >>> set sel [atomselect top "resid 1"]
> > >>> $sel get name
> > >>>
> > > gives....
> > >
> > > C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 O17......etc etc
> > >
> > > now using
> > >
> > >>> measure dipole $sel
> > >>>
> > > 0.0 0.0 0.0
> > >
> > This may be too obvious, but have you checked this?:
> >
> > $sel get charge
> >
> >
> > > and does this no matter what the molecule is including water. I'm not
> getting any measured vector for the measured dipole. It's probably something
> simple. Am I doing this the best way? I'm using the whole molecule as a test
> initially.
> > >
> > > Thanks
> > >
> > >
>
> --
> 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
>
>