[gmx-users] Forces in source code

[Berk Hess]

Hi,

Note that it is impossible to decompose a free energy (difference), which a PMF is,
uniquely into different energy or force components.
A free energy is not simply the sum of energy terms, but is the result of how
different energy terms together affect the accessible phase space.
The effect on a free energy of two energy terms is usually not simply the sum
of the two effects.

Berk

> Date: Mon, 13 Dec 2010 01:09:01 +0300
> Subject: Re: [gmx-users] Forces in source code
> From: magistrpetrus at gmail.com
> To: gmx-users at gromacs.org
> 
> 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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