[AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent

From: Yip Yew Mun <yipy0005.gmail.com>
Date: Thu, 18 Jun 2015 15:32:41 +0800


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 - 01:00:02 PDT
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