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

[Mark Abraham]

Hi,

For distance restraints, there is also an mdp section in which you must
choose values.

Mark
On 13/04/2015 4:42 am, <atsutoshi.okabe at takeda.com> wrote:

> 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
>
> 化学研究所(B42F-4110)
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