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

[Thomas Schlesier]

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.
Greetings
Thomas

> 
> 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,
> 
> 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.
>