Re: Protein Charge

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Jan 07 2019 - 10:17:32 CST

Just to be clear, the *system* as a whole should be neutral, but the
protein itself need not be (and frequently won't be). So one can very
easily have a situation where charged macromolecules will move in response
to an applied voltage, but the system as a whole is still net neutral.
Best,
Peter

On Mon, Jan 7, 2019 at 8:45 AM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:

> 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
>
>
>
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> *From: *Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
> *Sent: *Monday, January 7, 2019 11:56 AM
> *To: *namd-l <namd-l_at_ks.uiuc.edu>
> *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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