[gmx-users] scaling non-bonded interactions

[Kukol, Andreas]

FudgeLJ does only work when the pairs are generated automatically. If they are specified explicitly as in the Gromos forcefields, FudgeLJ has no effect.

Andreas
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 01 June 2011 20:38
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] scaling non-bonded interactions

Da-Wei Li wrote:
> I remember that 1-4 won't be scaled in the free energy code, right?
>

True, but the desired 10% scaling in this case can be applied by changing the
FudgeLJ and FudgeQQ values of the force field, I believe.

-Justin

> dawei
>
> On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Kukol, Andreas wrote:
>
>         Hello,
>         Is it possible to globally scale all non-bonded interactions by
>         a factor ?  I know there are energy exclusion groups, but that
>         is an all or nothing approach, while I would like to reduce
>         non-bonded interaction potentials to e.g. 10% of their normal value.
>
>         If this is not possible, I suggest to have this as an option in
>         the mdp-file.
>
>
>     You can do this with the free energy code.
>
>     couple-moltype = system
>     init_lambda = 0.9
>     couple_lambda0 = vdw-q
>     couple_lambda1 = none
>
>     Please note, though, that such settings will result in massive
>     performance loss, even for small systems.  There is an open issue on
>     the redmine server about this, but no resolution yet.
>
>     -Justin
>
>     --
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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