[gmx-users] Forces in source code

[Петр Попов]

Thank You!
I'll try to get what you writed, so, perhaps, I'll write about my
success or its lack!

12 декабря 2010 г. 4:42 пользователь Mark Abraham
<mark.abraham at anu.edu.au> написал:
>
>
> 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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