[gmx-users] Forces in source code

[Mark Abraham]

On 12/12/10, Петр Попов  <magistrpetrus at 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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