[gmx-users] Re: Generating initial coordinates and velocities from scratch
schlesi at uni-mainz.de
Thu Sep 17 16:08:11 CEST 2009
Look in the manual for 'genbox', with this tool you can make a box with
as many molecules you like.
For the velocity generation look under *surprise* 'Velocity generation'.
The manual is your friend, look in it.
> 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.
> Thank you,
> “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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