[gmx-users] vacuum with no pdc - problem

[Mateusz Nowak]

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