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

From: Norman Geist (
Date: Mon Apr 30 2012 - 00:29:21 CDT



there's is no need to fit a box shape to the proteins shape. The box is
periodic so it doesn't matter if part of the protein cross the boundaries.
One can do such thing to save computing time, for that reason there's also a
spherical boundary condition (see manual) , as one don't need to carry all
those additional waters, that needs to be simulated when the box is too big
for example. Also keep in mind that your box should be big enough, that the
protein doesn't interact with itself periodically, as this is mostly not
wanted. So the bottom line is, that one don't need a box that perfectly fits
the solute, if one doesn't have a molecule, that needs to be continued
periodically like a metal surface or a membrane for example. I think you
should inform about what periodic cell actually means.



Norman Geist.


Von: Xi Cheng []
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

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:

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: [] 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
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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