VMD-L Mailing List

From: Ana Célia Vila Verde (a.vilaverde_at_amolf.nl)
Date: Sun Sep 20 2009 - 08:01:12 CDT

Dear users,

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 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?

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
_______________________________________________________