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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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