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

[atsutoshi.okabe at takeda.com]

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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