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

[Manuel Valera]

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



  
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[gmx-users] wall_atomtype

[Manuel Valera]

Greetings to All

I have a question about a new feature in the cvs code
and I was wondering if there was anybody who could
give
me a hand of a bit of help.
Thanks in advanced.

I am working on a project that involves simulation of
confined water between two hydrophobic surfaces.
I noticed that recently there was an addition to the
gromacs source code that would allow for this kind of
simulations

I downloaded the cvs source code to try out this new
feature, ran a small simulation of water with pbc=xy
and no surfaces and could see the water evaporate as
was expected

The problems occurs when I need to add surfaces to the

simulation. There are some new variables that I don't
know how to set and I have not been able to figure
this out from the source code.

What are the appropriate values for wall_atomtype?
I want to have a LJ interaction between the wall and
the oxygen atom in
the water molecule.
How can I do this with this new feature?

In the function do_walls we have (file wall.c)

if (ir-wall_type == ewt93) {
  fac_d[w] = ir-wall_density[w]*M_PI/6;
  fac_r[w] = ir-wall_density[w]*M_PI/45;
} else if (ir-wall_type == ewt104) {
  fac_d[w] = ir-wall_density[w]*M_PI/2;
  fac_r[w] = ir-wall_density[w]*M_PI/5;
}

Where are these factor coming from, is there a
reference that I can look at?

What would be appropriate values for the variable
wall_density?

Would these be the appropriate changes to my
grompp.mpd file to get
this feature working of is there anything else that I
need to add?

pbc=xy
nwall=2
wall_type=9-3
wall_atomtype = ? ?
wall_density = ? ?

I apologized if these are too many questions!!

I realized this a very new feature and probably it is
not well tested, yet I would like to try it out and
see if I can use this for my project

Any help would be really appreciated.

Thanks a lot.
Kind regards,

Manuel Valera






   

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