[gmx-developers] rlist larger than L/2 in simple neighbor search
ggroenh at gwdg.de
Wed Oct 13 08:33:33 CEST 2010
On 10/12/2010 06:49 PM, Lee-Ping Wang wrote:
> Hi there,
> For the past few months, I've been adding a charge equilibration model
> to GROMACS (to be specific, QTPIE -- a refinement of QEq). For the
> model to work properly, each atom must "see" each other atom in the
> electrostatic interaction (it is a screened Coulomb interaction).
> This is easy enough to do with pbc = no; I just set all the cutoffs
> to zero, and add a new neighbor-list that includes excluded atom pairs.
Since we'd be interested in that, I would appreciate if you can keep us
informed of your progress.
> Now I would like to run the simulation with PBC turned on, which means
> either implementing Ewald summation or using cutoffs for the
> electrostatic interaction. When cutoffs are turned on (with or
> without PBC), the model goes haywire even with very long cutoff
> lengths. I haven't implemented Ewald summation for the screened
> Coulomb interaction, and I'm not sure if it's worth the effort if an
> easier fix is possible.
If I recall correctly, the screened Coulomb here means the overlap
integral between s-type Slater functions. This interaction behave as a
normal coulomb at large distances, so that coudl explain the issues with
increasing the cut-off. But an Ewald expression will be difficult as
well, since the all pairs-wise interactions are required to compute the
charge flow parameters. I have so far only seen it applied to molecules.
For non bonded system like a box of water, a direct charge flow between
atoms far apart is unlikely though. Could one not simply scale also the
charge transfer variables to zero with distance as well?
> As a quick fix, I changed the simple neighbor-searching code to set
> rcut = 1000000 when QTPIE is turned on.
> I am worried about the other possible consequences of my change; will
> this adversely affect the molecular dynamics or create artifacts in
> some unexpected way?
You will get the ordinary artefacts caused by cutoff, like ordering etc.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-developers