[gmx-developers] Re: Editing the GROMACS energy function

alex.bjorling alex.bjorling at gmail.com
Fri Aug 31 17:24:30 CEST 2012

You certainly have, thanks.

The function can indeed be written as an independent module, it just needs
the coordinates. So I guess that means that if I need to operate on all
coordinates I will have to run without domain decomposition?


Francesco Oteri wrote
> You can do simply writing your own function and executing it after (or
> before, it depends by the details of your modification)
> do_force (in md.c) simply modifying the f vector and printing the output
> after print_ebin (the function that actually prints results).
> Of course this approach is right just if your modification can be
> developed
> as an independent module.
> Regarding coordinates, because of domain decomposition, each node can
> access only to local atom data.
> ...
> I hope I've helped you :)
> Francesco
> 2012/8/31 alex.bjorling <alex.bjorling@>
>> I'm now in the exact same position as Radhakrishna describes here. After
>> posting the following, I did some more research and now have ways to get
>> both energy and force from a complicated operation over all coordinates.
>> http://gromacs.5086.n6.nabble.com/Adding-an-artificial-energy-term-for-structure-refinement-tp5000240.html
>> Has anyone been successful in making these modifications?
>> Best,
>> Alex

View this message in context: http://gromacs.5086.n6.nabble.com/Editing-the-GROMACS-energy-function-tp4669473p5000724.html
Sent from the GROMACS Developers Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-developers mailing list