[gmx-users] Calculating number density using g_density
Mark.Abraham at anu.edu.au
Tue May 29 07:39:06 CEST 2012
On 27/05/2012 2:00 AM, Andrew DeYoung wrote:
> It is possible to compute the number density using g_density, with the
> switch "-dens number". Do you know if this is the number density of
> molecules? Or is it the number density of atoms?
I'd expect atoms, but you should be able to test for this easily.
> Ideally, I would like to compute the number density of _molecules_.
> Specifically, I would like to use the center of mass of each molecule to
> represent that molecule's position. Then the center of mass of each
> molecule should be used to calculate the number density of molecules. Do
> you know if this is possible using any of the Gromacs utilities?
Not natively. g_traj -com can compute centers of mass of groups, which
you could assemble into a pseudo-trajectory using a script you wrote
yourself. g_density -dens number should then work on molecules as you
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