[gmx-users] How to add a repulsive harmonic potential

[atsutoshi.okabe at takeda.com]

Thank you for your help.
Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these ligands.
The reason why I add some ligand molecules(not one ligand) in simulation is to enhance ligand sampling.

I tried using [distance_restaints] below, not use [bonds] because of domain decomposition error. Then, the MD simulation could run normally without domain decomposition error!
[ distance_restraints ]
;ai aj type index type' low up1 up2 fac
13  63  1    1     1    20   100 100 10000

However, the distance between 13 atom and 63 atom seems to be less than 20 angstrom in every steps of MD simulation.
So I tried to change the fac value from 10000 to -10000, but the distance was less than 20 angstrom during MD simulation
Why the ligands were restrained less than 20 angstrom although I think I add repulsive force between these atoms?

Bests regards,
Atsutoshi Okabe


Hi,

If it's physical, then trying to suppress it arbitrarily does not seem
likely to lead to useful observations. If it's an unphysical artefact of
the model, then fixing the model seems more appropriate.

Mark

On Tue, Apr 7, 2015 at 7:35 AM, <atsutoshi.okabe at takeda.com> wrote:

> Thanks, Mark.
> So, do you have any good idea to avoid ligand aggregation in current
> released code?
>
> Best,
> Atsutoshi Okabe
>
>
> Hi,
>
> It seems like this is not a good idea after all. Things under a weak
> repulsive potential will move further away and run into such problems,
> because the domain decomposition needs to divide space geometrically.
>
> Mark
>
> On Mon, Apr 6, 2015 at 11:19 AM, <atsutoshi.okabe at takeda.com> wrote:
>
> > Hi Mark,
> >
> > Thank you for your help.
> > I use distance restraint implemented with [bonds] type 10 in current
> > released code.
> > [bonds]
> > 13 63  10  2  9  9  41.8
> >
> > However, I got the error message below.
> > Fatal error:
> > 1 of the 126679 bonded interactions could not be calculated because some
> > atoms involved moved further apart than the multi-body cut-off distance
> > (0.868598 nm) or the two-body cut-off distance (1.433 nm), see option
> -rdd,
> > for pairs and tabulated bonds also see option -ddcheck
> >
> > I think this is the reason why is that the distance between restraint
> > atoms of ligands to avoid aggregation is over two-body cut-off
> > distance(1.433nm).
> > The box size of simulation is 9.2*9.2*9.2(nM^3), so it is possible to be
> > over the cut-off value because the distance is the inter-moleculer
> distance
> > between ligands avoided aggregation.
> > Could you advice how I can solve this error?
> >
> >
> > Bests,
> > Atsutoshi Okabe
> >
> >
> >
> > You can use a distance restraint (see manual) implemented with [bonds]
> type
> > 10. In current released code, the atoms need to be within the same
> > [moleculetype], which would likely mean you need to aggregate the
> ligands'
> > topology definitions so that you can refer to atoms in different actual
> > molecules that are now within the same [moleculetype] Alternatively,
> there
> > is draft code for inter-molecular bonded interactions at
> > https://gerrit.gromacs.org/#/c/2566/, but nobody has yet tried that it
> > works.
> >
> > Mark
> >
> > On Fri, Nov 14, 2014 at 10:45 AM, <atsutoshi.okabe at takeda.com> wrote:
> >
> > > Dear all
> > >
> > > To avoid ligand aggregation under higher concentration, I would like to
> > > introduce a weak repulsive potential term between the specific(e.g
> > > nitrogen) atoms of ligand molecules in the Protein/Ligand/Water system.
> > > This potential set as below.
> > > U(R) = K(R-R0)^2, if R<R0 (repulsive potential)
> > > U(R) = 0, if R>R0
> > >
> > > Could you tell me how to add the repulsive harmonic potential in MD
> > > simulation?
> > >
> > > Bests,
> > > Atsutoshi Okabe

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