[gmx-users] Stockmayer fluid, extended dipole without rotation

Manuel Valera valeraml at yahoo.com
Wed Dec 24 06:42:30 CET 2008

Greetings to All,

I am working on a simulation of a Stockmayer fluid under electric fields and I thought I would 
ask for some help  regarding the implementation of this system in gromacs as I have not 
been able to figure this out from the user guide. Thanks in advanced.

The system is composed of stockmayer particles (Lennard Jones plus dipole interaction)
 with the dipole always aligned along the z axis. There is no rotation of the dipole.

To do this gromacs I could use extended dipoles, i.e. a linear molecule composed of 3 particles.
One big particle with diameter 1 and lennard jones interaction.
Two particles without mass very close to each other with charges q and -q, these two particles
would be inside the big particle and would be responsible for the dipole interaction. 

By defining a linear  molecule in this way I could probably get the same effect of a stockmayer fluid.

Question 1;
How can I do this using virtual particles as I only have one real particle and 2 dummies and 
gromacs requires at least 2 particles to defines the location of the dummies?

Question 2
How can I constrain the molecule to be always aligned along the z axis.

I really appreciate any help on this and thanks a lot for your reply.

Feliz Navidad!!

Manuel Valera


More information about the gromacs.org_gmx-users mailing list