[gmx-users] Box size

Dallas Warren dallas.warren at monash.edu
Tue May 8 06:29:53 CEST 2018

Bit unclear from your description, but do you have two sheets which
are meant to meet up with each other in the x-y plane, so you get two
infinite sheets?  And currently they don't exactly meet up?  If so,
then you need to rotate them (using gmx editconf) so that they are
perfectly aligned.  Then you can use VMD with the periodic image
display option, and adjust the box size around it, so that that atoms
at one edge matches up with the correct distance through the PBC to
the other edge.  Then the z direction probably will need to be at
least 6nm, since they are already 3nm apart, then through the PBC you
would probably want them at least that distance apart.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 8 May 2018 at 03:24, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> Hi,
> I have two nanosheet structure and they are infront of each other and about
> 3 nm far from each other.
> I have some problems in fitting the box size. I used many options
> triclinic, -box,... to fit the size, but it's not possible. The problem is
> that atoms in ZnS nanosheet are not aligned and are up & down and this
> makes the minus z dimension coordination and i can't use -box option. How
> can i solve this problem? I want to make box size as fit as possible to
> have the least solvent molecules in next step.
> Regards
> -Roja
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