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

Yun Shi yunshi09 at gmail.com
Tue Nov 27 03:25:47 CET 2012

I did hope the ions will move out eventually.

But after my ~70ns of conventional MD (with duplicate MD runs and the
protein as a dimer with identical sequence), they were still there in
the binding site.

So I assume it would be much better to start without any salt ions
beside my ligand.

Could anyone suggest a way around this?


On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> On 2012-11-26 21:28, Yun Shi wrote:
>> 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.
>> Thanks,
>> Yun
> Maybe your assumption is wrong?
> Run a long MD simulation and you will find out.
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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