AW: AW: Set up NPT simulation in cubic PBC-box

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Apr 30 2012 - 00:21:02 CDT

Hi,

 

as I already said, by using the parameter useconstantarea or
useconstantratio, you can hold your x-y area as a square, but not Z also.
Maybe we can give you advice, if you tell us why you want to have a cubic
cell, why should that be important?

 

Norman Geist.

 

Von: Xi Cheng [mailto:xichengeva_at_gmail.com]
Gesendet: Freitag, 27. April 2012 17:20
An: Norman Geist
Betreff: Re: AW: namd-l: Set up NPT simulation in cubic PBC-box

 

Hi Norman,

 

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?

 

Thanks,

Xi

 

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

 

Hi,

 

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?

 

Thanks,

Xi

 

 

 

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