[gmx-users] adding Ca2+ ions to the solvent (either randomly or restrained)

m r gmstma_rezaei at yahoo.com
Mon Sep 12 16:03:19 CEST 2011

  Dear all,
In an attempt to simulate the effect of adding calcium ion to the solvent
around my protein of interest, I wonder how to add Ca2+ ions in the 
following cases (in GROMACS 4.5.4):
1) adding Ca2+ ions randomly distributed in the solvent;
2) adding Ca2+ such that it is initially restrained in vicinity of some 
specified groups on the surface of my protein (I mean: something similar to
restraining the ligand in a search box during its docking to a receptor).
Any valuable comments are highly appreciated.
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