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

[atsutoshi.okabe at takeda.com]

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