[gmx-users] puting things in

[Mark Abraham]

Itamar Kass wrote:
> Hi Mark,
> 
> I thought I was clear. I want to have a gro file in which all the 
> peptide are in the same side of the membrane and with the minimum 
> distance between them (lowest distance between mirror images).

Right, so we didn't need to know anything about your previous 
simulation... this is what being clear is all about! You still seem to 
be confusing "minimum distance between them" where "them" = "your four 
peptides", and the distance between periodic (not "mirror") images.

If I guess correctly, then you need to use some kind of molecule builder 
to generate a structure file that has your peptides close together, then 
build your monolayer with respect to that, then add your solvent. 
Obviously, you've already determined that having your peptides close 
together will let you study what you want to study.

Mark