VMD-L Mailing List
From: Ana Vila Verde (a.vilaverde_at_amolf.nl)
Date: Thu Apr 17 2008 - 02:54:08 CDT
- Next message: Deanna Fleming: "Replica watch is a perfect gift"
- Previous message: cong chen: "atomselect"
- Next in thread: Olaf Lenz: "Re: measure hbonds between protein and water - problem with periodic boundary conditions"
- Reply: Olaf Lenz: "Re: measure hbonds between protein and water - problem with periodic boundary conditions"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Dear VMD users,
I am trying to use the command measure hbonds to calculate the number of
hbonds between a molecule and water from a simulation with PBCs.
However, very often my molecule "sticks out" of the water box, and when
that happens I get an inaccurate count of hbonds. I checked the mail
list archive for a possible solution and didn't find any. I also don't
think that unwrapping my trajectory is a solution to the problem,
because the density of the "real" water molecules will be lower around
my molecule and I will also not get an accurate count.
I thought I'd ask whether any of you would share a script to get around
this problem before I go and code my own.
Thank you for you attention. Best regards,
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: +31-20-6081392 Fax: +31-20-6684106 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 _______________________________________________________
- Next message: Deanna Fleming: "Replica watch is a perfect gift"
- Previous message: cong chen: "atomselect"
- Next in thread: Olaf Lenz: "Re: measure hbonds between protein and water - problem with periodic boundary conditions"
- Reply: Olaf Lenz: "Re: measure hbonds between protein and water - problem with periodic boundary conditions"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]