[gmx-users] ion jumping out of water box

Erik Marklund erikm at xray.bmc.uu.se
Mon Jan 10 20:12:48 CET 2011

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 

Try trjconv -pbc nojump.

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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