[gmx-users] Periodic Boundary condition

Rohit merohisg at yahoo.co.in
Tue Feb 5 06:17:08 CET 2008

Thanks for valuable suggestions.
The simulation cell has dimension of 5.8nmX5.8nmX3*5.8nm.. And a single layer consists of 400 atoms and thus has a dimension of 5.46nmX5.46nm in XY plane. Do you think system size is small enough for long-range 
non-bonded interactions and/or velocities to traverse the vacuum gap?
having the information of surface dimension, can I still use distance restraints to hold all my molecules of tetrahydrofuran?

And the physical model is comparable with what people have published. Moreover, People have done some monte carlo simulation studies, there they have used a repulsive (reflecting) wall to apply periodic boundary condition only in a plane.

And I think not having a proper boundary condition in my system is a cause of error in my results.


Mark Abraham <Mark.Abraham at anu.edu.au> wrote: Rohit wrote:
> Hi Mark,
> Please accept my apology for not putting a descriptive subject line.
> My query is regarding the periodic boundary condition only. I read from 
> email archives regarding implementing periodic boundary conditions in XY 
> plane and not in Z direction and one can do that by increasing the size 
> of box in z direction by 2-3 times and thus creating a vacuum boundary. 
> However, in my case molecules are still moving to other side (i.e -Z) 
> and interacting with the gold surface. But what I want is interaction 
> only at the top surface not the opposite surface.

This suggests that your system size is small enough that your long-range 
non-bonded interactions and/or velocities are big enough that you can 
traverse the vacuum gap. Is your physical model comparable with 
published studies? If not, check there first.  Other than increasing 
your gap or playing with your physics, there's not much one can suggest. 
You could use distance restraints on all particles that keep them within 
a certain distance of an atom the surface, but this might be problematic 
if the surface's area is large with respect to the restraint distance. 
I'd much rather fix my physics than do this, however.

> I guess now problem is lucid.
> Please help me if anything can be done to have a system where molecules 
> can interact only at the top surface of gold layer not the below surface.

gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

 Bollywood, fun, friendship, sports and more. You name it,  we have it.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080205/4907c1d2/attachment.html>

More information about the gromacs.org_gmx-users mailing list