[gmx-users] Ions drifting

Johnny Lu johnny.lu128 at gmail.com
Thu Dec 18 15:07:31 CET 2014


If the Na or Cl ion don't strongly bind to the protein, as described by the
force field, then they might not always bind to and stay with the protein
in the simulation.
If that is what you want, I guess you can artificially add a restraint to
make the ion to stay closer to the protein ... I'm not sure about the
consequence.

On Thu, Dec 18, 2014 at 5:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 12/17/14 11:47 PM, jani vinod wrote:
>
>> Dear Johnny,
>> I  want to make the Na or Cl- ion always stay with the protein.
>> I tried -pbc mol option ans selecting group as Protein_ion but it didn't
>> work.
>>
>>
> This should be simple to do with trjconv -center -pbc mol -ur compact
>
> Choose Protein for centering and System for output.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
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