[gmx-users] Re: Problem with restraint in lipid membrane

[Francesco Tordini]

Thank you David for your advice. Now I've created two distinct files 
for position restraint for dppc and dppe. It seems to work.
I've tried to make an energy minimization on my system, and in fact
I find the new energy contributions for position restraint.
What is still unclear it is that the structure
observed as a result of minimization shows some chains that are located
out of the box boundaries. I get the same result with the original
dppc64.pdb file and also with molecular dynamics.
My question is: is this problem anyway related to the following
entry in log file:

"Removing pbc first time
 Done rmpbc"

What this expression means?
Maybe it's a trivial question, but i'm quite a beginner with gromacs

Cheers

Franz

=====================================================================

Dr. Francesco Tordini
Università di Milano-Bicocca
P.zza della Scienza, 1
20126 Milano
tel.  0264483473
cell. 3282794451
email tordini at tiscalinet.it