On 27/05/2012 2:00 AM, Andrew DeYoung wrote:
Hi,
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
intend.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
