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

Lum Ngwagia lumngwegia at yahoo.com
Wed Sep 16 20:26:01 CEST 2009

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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