[gmx-users] Periodic boundary problem

Haberl Florian Florian.Haberl at chemie.uni-erlangen.de
Thu Nov 4 10:14:21 CET 2004

dear gmx-users,

I want to perform an md simulation with an dimer proteine.
after performing em/pr/ or md the dimer is seperated in
two monomers and one of this is outside my waterbox
(viewed by gopenmol).

After some search i found the trjconv command should fix this
problem which is caused through periodic boundary conditions
(i guess this is the problem).

So an -pbc nojump should fix it, but this is not always so,
sometimes it^s still outside the box and i don^t know why.

Tried this now with several input files but always same behavoir.

Any suggests how to fix this?



 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de


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