VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 18 2010 - 14:34:29 CST

david,

On Thu, Nov 18, 2010 at 1:57 PM, David Wedner <wedner.david_at_yahoo.com> wrote:
> Hi
> I am running an NPT simulation and accordingly the volume is not fixed
> I would like to know if vmd take in consideration the change in volume in
> calculations that require the volume "such as g(r)" ?

that depends on the individual implementation
and availability of the proper information.

> and if not, what volume will be considered ?

the g(r) will definitely consider change of volume,
_if_ the information is available. if you use a file format
that does not contain volume information, or one
but it requires an orthorhombic cell. tilted cells
are not supported (you should get an error message).
i know this for certain, since i wrote that code. ;-)

for other pieces it depends on the requirements
(and available time) of the respective author(s).
in many cases it is irrelevant.

often the problem is not the volume itself,
but general support for periodic boundary
conditions (or lack thereof). this whole field
is still in flux and a lot of what is or will be
available depends on valid user requests.

cheers,
    axel.

>
> Thanks
> David
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.