[gmx-users] How to avoid adding ions close to ligand

Yun Shi yunshi09 at gmail.com
Mon Nov 26 21:28:02 CET 2012

Hi everyone,

I am doing conventional MD of a protein-ligand system with a mobile
loop as part of the binding site.

Presumably, the positive Arg side chain on the mobile loop will
eventually move towards the negative carboxylic group on my ligand.
But I found the addition of NaCl (0.15 M conc.) had some effect on
this movement, since the random addition could put Na+ or Cl- ions
between the mobile loop and my ligand.

I tried generating a index containing only SOL far not close to my
ligand, but apparently genion requires a continuous solvent group. So
is there any other way to achieve this? Trying different numbers for
-seed option seems inefficient and is dependent on luck.


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