[gmx-users] Velocity Distribution Calculation

Justin Lemkul jalemkul at vt.edu
Thu Aug 7 15:04:39 CEST 2014

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.


> Thank you very much.
> Best,
> Jason
> 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


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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list