[gmx-developers] Beginning developing Gromacs

Christopher Burger christopherhburger at gmail.com
Tue May 1 23:46:36 CEST 2007


I'm a complete newcomer to Gromacs, so please excuse my ignorance.

What I am attempting to do is to modify mdrun in such a way as to
modify the structure of a loaded molecule every n iteration steps. The
point is to load a molecule which is very simple, but incomplete, and
then, every n steps, reconstruct the molecule and calculate the
electrostatic field around in the (reconstructed) molecule.

What I need is a starting point.

I would expect some structure to hold all information about the
simulated molecule (atom bonds, atom positions, atom masses, atom
velocities) at every time step, but was unable to find one. Is there
such a structure, and in that case, which structure is it? If not,
what approach should I choose in order to modify the molecule?

Also, how is the electrostatic field inside and around a molecule computed
in Gromacs? At what point does that computation take place? What
parameters does it require?

I was initially considering working in do_md inside md.c. Does this make sense?

Best regards,


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