[gmx-users] Velocity Distribution Calculation

朱文鹏 jasonzhu925 at gmail.com
Thu Aug 7 15:02:47 CEST 2014

Dear all,

I posted it days before. But no one replied.

I am wondering if someone has any suggestions about calculation of velocity

Thank you very much.


2014-08-05 23:55 GMT-04:00 <jasonzhu925 at gmail.com>:

> Dear all,
> I am a new user of GROMACS. Now I am using it on water permeability
> through a nano-channel. The pressure difference is applied by adding
> acceleration to water molecules in a periodic simulation box. To get the
> flow rate of water, I need to the number of water molecules through the
> channel or spatial velocity distribution in different regions.
> I used to do similar simulations by LAMMPS. LAMMPS provides the function
> of "count (region, group)" or the command of "fix ave/spatial" for counting
> atom number or velocity distribution. I am wondering how I can do it in
> GROMACS. Does it have the same commands? I went over the manual and saw
> commands of "g_traj" and "g_spatial". Are they what I am looking for?
> Thank you very much for your attention.
> Best,
> Jason

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