On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:
Hi
I want to do Coarse-Grained simulation in Gromacs. I have one CG force
formula, which I plan to implement by adding a short code in do_force()
routine in Gromacs 4.0.7 source code.
After browsing through the do_force() code, I am now familiar with data
structure relevant to add the new force. I mean, I can specify new force
by adding to f[indx][XX] and so on.
But I am not very sure about potential, whether do I have to explicitly
specify the potential on atoms due to this force or gromacs
automatically takes care of it by knowing the forces on each atoms?
You will need to add that yourself if you want the reported potential to
be accurate. GROMACS uses the given parameters in its inner loops to
calculate energies and forces. The former are not reverse-engineered
from the latter. If the potential is never used, however, then you can
forget about it...
Mark
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