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 -- This message has been scanned for viruses and dangerous content by [ https://urldefense.proofpoint.com/v2/url?u=http-3A__www.efa-2Dproject.org&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=ILzoZkBQwl1NU0ot9TlDgtr2uJrObVxgbHaI2K9LbTw&s=ycJxk2lepzyMOiRhsIxpqYBRxJNBZ66pf0F_y-oEipA&e= | KNTU Antispam System (E.F.A. Project) ] , and is believed to be clean.
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