From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Mon Jan 07 2019 - 07:37:06 CST
Yes, the sum of charges of your structures should be zero, it is necessary.
By the way, you can add some ion to structure in order to achieve a neutral charge.
Good luck, ashkan
Sent from Mail for Windows 10
From: Ashkan Shekaari
Sent: Monday, January 7, 2019 11:56 AM
To: namd-l
Subject: namd-l: Protein Charge
Dear Users,
When I simulate my protein in the NVT ensemble and apply an electric field,
the protein begins to move along the direction of the field. Which means that
the protein is not charge-neutral.
Is my simulation accordingly wrong?
Is it necessary for a protein to be charge-neutral in MD simulations?
-- Regards, Ashkan Shekaari, Ph.D Candidate in Solid State Physics, K. N. Toosi University of Technology, Tehran, Iran -- This message has been scanned for viruses and dangerous content by KNTU Antispam System (E.F.A. Project), and is believed to be clean.
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