On 12/12/10, Петр Попов  <magistrpet...@gmail.com> wrote:
> Hello, dear gmx-users.
> 
> I want to decompose PMF, but I can't use -rerun option for this
> because I get this PMF due to pull force. And also .trr files are
> large to do md with different energy groups to get PMF.
> So, I need to adopt source code for this task.
> Could you help me and give me any advices? - in what .c files are
> forces and pull force are evaluated? Or from what I must start?
> 

To do this kind of group-wise decomposition of forces you need to give 
different force arrays to the evaluation of different neighbour lists. I've 
posted replies to this before, so please search for it. To get a handle on how 
things work, set up a tiny box of water molecules using a plain Coulomb cut-off 
and step through a serial GROMACS mdrun in a debugger. Then move the simulation 
gradually closer to the setup you have in mind and note the differences in how 
the force arrays are handled - they'll be different in parallel and presumably 
with pulling. Then you'll have to mimic the way the ebin code stores group-wise 
non-bonded energies to store group-wise non-bonded forces. Then you'll want to 
write them out to separate .trr files.

Mark
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