[gmx-users] vacuum with no pdc - problem

Mateusz Nowak mynowak at cyf-kr.edu.pl
Fri Apr 19 16:01:24 CEST 2002

Hi Gmx-users.

I try to mimimize a protein molecule consisted of 3 unbound chains in
vacuum without (pbc = no in parameter file). All 3 chains are defined as
one molecule in topology file (-merge option in pdb2gmx). Unfortunately
just after starting the minimization (in the first step) second and third
chains "jump" to somewhere in space, few nanometers from initial

What can be a reason for this?


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