[gmx-users] exclusions for a specific model

Cristiano De Michele cristiano.demichele at roma1.infn.it
Wed Mar 17 11:20:54 CET 2010

Dear GROMACS users,
I created a custom topology file to
define a molecule composed of 5 sites.
Two sites are real massive sites (but for them
C6=C12=0 and their charge is 0, hence they do not interact
with sites of same type on other molecules),
while remaining three sites are virtual sites.
Two of these virtual sites carry a charge (but C6=C12=0), while the  
third one has no charge and
interact with other virtual sites of same type through VdW interactions.
With this topology real sites do not interact with
other real sites but they are used only to carry a given mass.
My question is: is it possible to exclude these real sites from
non-bonded forces calculations (and neighbors search) to speedup
simulations? unless having C6=C12=0 and 0 charge for real sites
they are automatically excluded...

thanks for your help
in advance,
Cristiano De Michele, Ph.D.
Department of Physics                             Tel.  :  +390649913524
University of Rome  "La Sapienza"        Fax  :  +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
homepage: http://pacci.phys.uniroma1.it/
"Shoot for the moon. Even if you miss, you'll land among the stars."

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