Re: Protein Charge

From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Mon Jan 07 2019 - 07:42:25 CST

Thank you so much, dear Soroush.

-- 
Regards, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "soroush ziaei" <soroush.ziaei7337_at_gmail.com> 
To: "namd-l" <namd-l_at_ks.uiuc.edu>, "shekaari" <shekaari_at_email.kntu.ac.ir> 
Sent: Monday, January 7, 2019 5:07:06 PM 
Subject: RE: namd-l: Protein Charge 
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 [ https://go.microsoft.com/fwlink/?LinkId=550986 | Mail ] for Windows 10 
From: [ mailto:shekaari_at_email.kntu.ac.ir | Ashkan Shekaari ] 
Sent: Monday, January 7, 2019 11:56 AM 
To: [ mailto:namd-l_at_ks.uiuc.edu | 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 
-- 
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