[gmx-users] Generating initial coordinates and velocities from scratch.

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 17 15:54:38 CEST 2009

Lum Ngwagia wrote:
> Hello everyone,
>        I have been struggling to find a way to supply initial 
> coordinates and initial velocities to a molecule like pentane. I want to 
> add about 2500 molecules of pentane to a box, but all these molecules 
> must have initial positions and velocities. I have used ghemical to draw 
> the molecule and converted it to the pdb format, so I have only 
> coordinates for one molecule.
>        How do I generate initial coordinates and velocities for the 
> other 2499 molecules from scratch? Please, help me out.

Use either genbox or genconf.  To get velocities, set "gen_vel = yes" in the 
.mdp file.


> Thank you,
> Lum
> *    */*“If you’re too busy to pray then you’re busier than God wants 
> you to be. There’s nothing beyond the reach of prayer except that which 
> is outside the will of God.”* *- A man of God.*/**
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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