[gmx-users] ion jumping out of water box

[Erik Marklund]

גדעון לפידות skrev 2011-01-10 20.08:
> Hi all,
> I have been running simulations of a soluble protein bound to a pair 
> of calcium ions. I have been running this simulation in 4 nano second 
> intervals. everything looks fine until the 14th nano second when one 
> of the ions just jumps out of the water box. pbc-mol does not correct 
> the problem.
> I am using gromac version 4.0.7,
> Does anyone know what the problem could be?
> Thanks,
> Gidoen
I strongly suspect nothing is wrong. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Try trjconv -pbc nojump.

-- 
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/