VMD-L Mailing List
From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jul 27 2017 - 12:42:39 CDT
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- In reply to: jrhau lung: "Protein move out of the water box in a QwikMD setup MD simulation using explicit solvent condition"
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Dear Jrhau,
there is nothing wrong with the protein "moving out of the box" as QwikMD
sets the periodic boundary conditions.
Please find a very nice answer from Norman Geist
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/3351.html
Best wishes
João
On Wed, Jul 26, 2017 at 6:37 PM, jrhau lung <jrhaulung_at_gmail.com> wrote:
> Dear VMD friend:
> If my protein move out of a 15 angstrom water box in a QwikMD setup MD
> simulation, is there any way to avoid this in the preparation process of
> the simulation, Thanks.
>
> sincerely,
>
> Jrhau
>
>
-- ……………………………………………………... João Vieira Ribeiro Theoretical and Computational Biophysics Group Beckman Institute, University of Illinois jribeiro_at_ks.uiuc.edu +1 (217) 3000380 <(217)%20300-0380> -- ……………………………………………………... João Vieira Ribeiro Theoretical and Computational Biophysics Group Beckman Institute, University of Illinois jribeiro_at_ks.uiuc.edu +1 (217) 3000380 <(217)%20300-0380>
- Next message: Mayne, Christopher G: "Re: ffTK: neutral pyruvate group and charged pyruvate group at beta-D-mannose"
- Previous message: Steven(Yuhang) Wang: "Re: mol pdbload failing"
- In reply to: jrhau lung: "Protein move out of the water box in a QwikMD setup MD simulation using explicit solvent condition"
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