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
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