[gmx-users] Re: vacuum with no pdc - problem

Mateusz Nowak mynowak at cyf-kr.edu.pl
Fri Apr 19 16:16:43 CEST 2002

Hi again

Please ignore this post. In fact pbc = no was commented in parameter file,
and when I uncommented it everything ran smoothly.


On Fri, 19 Apr 2002, Mateusz Nowak wrote:

> 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
> positions.
> What can be a reason for this?
> Mateusz

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