[gmx-users] Small V.S. Large simulation box.

Yang Ye leafyoung81-group at yahoo.com
Thu Mar 9 09:00:53 CET 2006

As being iterated for many times in this list, use of PME shall be only
applicable to box of certain size, not too small. The default grid size
for PME is 0.095, with a 0.2nm box, there is only two points. And I
don't think this can be lifted simply by further decreasing grid size.

Yang Ye

Yinghong wrote:
> Dear Gmxers:
> For some particular reasons, I need to adopt a very small simulation
> box, in which box boundary is only ~0.2nm to the surfuce of solute,
> and PME is used as coulombtype.
> Roughly speaking, I want to observe the displacement of some atoms,
> which is however 30% lower than expected. If I enlarge the box,
> everything goes smoothly. Has anybody ever used such a small box? Any
> suggestion will be greatly appreciately.
> As I think, Maybe, the problem is from periodic boundary condition and
> long-range interactions treatment? But I can not find the relevant
> information both in manual and in mailinglist.
> Thanks.
> Xie Yinghong
> Hong Kong University
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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

More information about the gromacs.org_gmx-users mailing list