[gmx-users] Positioning ions consistently

Lieven Buts lieven at ultr.vub.ac.be
Wed Apr 10 10:39:21 CEST 2002

  I am trying to compare a number of small variations of
the same protein structure. The protein has a net charge of
-9 (well, -8.999999, anyway). When I add 9 Na ions to
the different variations, some of them are put in very
different positions. This might be an additional source
of variation between the starting structures.

  Would it be necessary/useful/pointless to try and
position the ions more consistently for the different
structures? Or maybe to leave the ions out altogether?

Lieven Buts
Vrije Universiteit Brussel

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