From: Xi Cheng (xichengeva_at_gmail.com)
Date: Fri Apr 27 2012 - 10:22:56 CDT
Thanks for your reply.
I want to simulate a sphere shape protein in the solution in NPT condition.
I tried to fix the ratio between x and y, and start system with cubic PBC box.
However, the resulting system has long box length along z; twice as those along x or y.
How can I keep the box cubic?
Or is there any other way that I can run NPT simulation for sphere shape protein?
On Apr 27, 2012, at 12:42 AM, Norman Geist wrote:
> Hi Xi,
> as far as I know, u can only fix the ratio between x and y. Maybe we can help you, when you explain what you want to do, and why you want to have an exactly cubic box.
> Norman Geist.
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Xi Cheng
> Gesendet: Donnerstag, 26. April 2012 23:23
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Set up NPT simulation in cubic PBC-box
> Is it possible to allow the three orthogonal dimensions of the periodic cell to fluctuate
> and keep the ratio of the unit cell in x-y/y-z/z-x plane constant at the same time?
> Or is there any other way to run NPT simulation in cubic PBC box?
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