Hi,
The key thing is to keep the charge in your overall box 0. So I would add 2
Cl- ions and no Na+ ions.
This way your system is neutral overall (a requirement for PME - Amber
would force neutrality otherwise, by smearing out excess charge over all
atoms in the system) and your concentration is in line with experiment.
I don't think it would really matter much in your system whether you have a
few more ions or not in terms of comparing to experiment.
Marc
On 18 June 2015 at 08:32, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi,
>
> I’m seeking help on a dilemma:
>
> I have a peptide that has a net charge of +2, 1000 explicit solvent
> molecules and 1 Na+ and 1 Cl- ions.
>
> My question is, the NaCl was added to the solvent box to mimic the
> experimental salt concentration. However, this would result in my
> simulation system having a net charge of +2. Therefore, should I or should
> I not add 2 more Cl- ions to neutralise the system (since that would also
> mean increase my conc of ions in the solvent box)?
>
> Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry &
> Biological Chemistry
> School of Physical & Mathematical Sciences | Nanyang Technological
> University | Singapore 639798
> Tel: (+65) 97967803 | Email: yipy0010.e.ntu.edu.sg | GMT+8h
>
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Received on Thu Jun 18 2015 - 01:30:02 PDT
