[gmx-users] ion jumping out of water box

jalemkul at vt.edu jalemkul at vt.edu
Mon Jan 10 20:14:35 CET 2011

Quoting ????? ?????? <glapidoth at gmail.com>:

> 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?

Correcting for periodicity may require more than one attempt at using  
trjconv.  using trjconv -pbc nojump, or trjconv -center may be  
necessary, either alone or in conjunction with other iterations.   
Unfortunately, trjconv takes a bit of experimenting to get working  
properly, and there is no clear how-to to treat the periodicity of any  
one system.


> Thanks,
> Gidoen

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