From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Apr 30 2012 - 00:21:02 CDT
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?
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
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
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
On Apr 27, 2012, at 12:42 AM, Norman Geist wrote:
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.
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
Betreff: namd-l: Set up NPT simulation in cubic PBC-box
Is it possible to allow the three orthogonal dimensions of the periodic cell
and keep the ratio of the unit cell in x-y/y-z/z-x plane constant at the
Or is there any other way to run NPT simulation in cubic PBC box?
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:55 CST