From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 20 2009 - 13:44:03 CDT

2009/9/20 Ana CÚlia Vila Verde <a.vilaverde_at_amolf.nl>:
> Dear users,

dear ana,

> I'm calculating the water density around a sugar molecule using the volmap
> command but I obtain values of order 1e+23 to 1e+28, which clearly don't

this may be a stupid question, but are you certain that you see 1e+23
and not 1e-23?

> make any sense. I've double checked my algorithm looking for possible
> sources of error, but so far nothing. I'm sure I must be missing something;
> can someone perhaps point me in the right direction?

i cannot see any obvious problem in what you do below, but it is
hard to track down things like this from remote. can you upload a
set of example files, ideally a small one, to the VMD BioFS on
BioCoRE, so that somebody can try and re-run your analysis, to
reproduce and eventually debug the problem?

it would also be helpful to let people know, on what platform you
are running on and with what version of VMD exactly you see this.

thanks,
    axel.

>
> Here it is a summary of what I do:
> - wrap the water around the main molecule (a sugar in this case) using
> pbctools
> - at each frame, translate and rotate all molecules so that the sugar is
> in the same approximate position/orientation in all frames and is
> centered at 0 0 0
> - compute the density map using the following commands:
>
> set sel [atomselect top "(within 3.5 of type OH OS) and type OW HW"] ;#
> select all water molecules within 3.5 of the sugar atoms
>
> volmap density $sel -weight mass -res 1.0 -minmax {{-10 -10 -10} {10
> 10 10}} -mol top -allframes -combine avg -o out.dx
>
> $sel delete
>
> Thank you for any help you can provide.
>
> Best wishes,
>
> Ana
>
>
>
> --
> _______________________________________________________
> Ana Vila Verde
> Post-doctoral scholar
> FOM Institute for Atomic and Molecular Physics [AMOLF]
> P.O.Box 41883
> 1009 DB Amsterdam
> The Netherlands
> Phone: +31-(0)20-754-7104
> Fax: +31-(0)20-754-7290
> E-mail: a.vilaverde_at_amolf.nl
>
> University of Minho
> Physics Center
> Campus de Gualtar
> 4710-057 BRAGA
> Portugal
> E-mail:avilaverde_at_fisica.uminho.pt
> _______________________________________________________
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.