On 8/7/14, 7:02 AM, 朱文鹏 wrote:
Dear all,
I posted it days before. But no one replied.
I am wondering if someone has any suggestions about calculation of velocity
distribution.
Select groups using g_select, extract velocities with g_traj, and create
distributions with g_analyze.
-Justin
Thank you very much.
Best,
Jason
2014-08-05 23:55 GMT-04:00 <jasonzhu...@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
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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