From: Bo Liu (boliu_at_ks.uiuc.edu)
Date: Wed Jan 19 2011 - 16:31:22 CST
Hi Joyce,
I think -0.4 e is OK for the system to run w/ PME.
Another option could be to pick up a 'far-away' ion and modify its partial
charge in the .PSF file just to neutralize the system.
Cheers,
Bo
On Wed, Jan 19, 2011 at 10:17 AM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
> Hi all,
>
> I'm simulating a protein where its CYS is deprotonated and bound to Zn2+.
> I did some modification to the topology file. After the modification, CYS'
> charge is -0.8 while Zn2+ has a charge of 1.2.
> When I evaluate my system charge with the command below:
>
> set sel [atomselect top all]
> eval vecadd [$sel get charge]
>
> The charge of my sys tem is -0.39999932795763016.
> I wana run my system in PME. So, is there any way I can neutralize my
> system? Or it's ok for me to proceed to the simulation without neutralizing
> my system?
>
> All suggestion are welcomed.
>
> Thanks.
>
> Regards,
> Joyce
>
-- ======================================== Bo Liu Theoretical and Computational Biophysics Group 3027 Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Urbana, IL 61801 http://www.ks.uiuc.edu/~boliu ========================================
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