Thank you a lot for your answer.
I did a simulation in explicit water and here I added counterions. Now I would like to try to reduce computational time and so I trying to look at implicit simulation..
Il giorno 30/mar/2011, alle ore 19.13, Jason Swails ha scritto:
> Implicit solvent doesn't typically use explicit counterions. If you're just
> looking for elecrostatic screening, look at the saltcon variable for GB, or
> istrng for PB.
>
> If it turns out that you need explicit counterions for some reason, consider
> using explicit solvent, or look carefully through the literature to see how
> people have handled this case. Be prepared for careful validation of your
> approach in this instance...
>
> To actually answer the question, now: counterions are added via the
> "addions" command documented in the manual.
>
> Good luck,
> Jason
>
> On Wed, Mar 30, 2011 at 10:03 AM, Elisa Frezza <elisa.frezza.gmail.com>wrote:
>
>> Dear all
>>
>> I am performing an implicit simulation of a charged peptide linked to a
>> porphyrin and I would like to include counterions.
>> How can I do? How can I screen these charged residues?
>>
>> Thank you
>>
>> Elisa
>>
>>
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Mar 30 2011 - 10:30:05 PDT
