[gmx-developers] rlist larger than L/2 in simple neighbor search

Lee-Ping Wang leeping at MIT.EDU
Tue Oct 12 18:49:47 CEST 2010

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.


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.


As a quick fix, I changed the simple neighbor-searching code to set rcut =
1000000 when QTPIE is turned on (normally forbidden under normal GROMACS run
conditions).  This brings the charges back to normal in a periodic box, plus
I now get complete uniformity of the charges in crystalline systems (e.g. in
FCC NaCl, the charges on the Na atoms are all the same).  I think this works
because simple neighbor-searching with an infinite cutoff length has the
effect of counting every neighbor once while still following the minimum
image convention.  I have verified this by looping through the atoms in the
neighbor list, and counting the number of interactions as well as printing
the shifted interatomic distances for a water box.  I consistently count
N*(N-1) interactions for a N-atom box, and the shifted interatomic distances
are consistently under half of the box diagonal.


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?  I am aware that this will lead to situations where a
solvent molecule may see both sides of a larger solute, but I can accept
those relatively small effects.  My main goal is to run NPT dynamics on a
QTPIE water model and verify physical properties like density, dielectric
constant, etc.


Thanks a lot for your help!


-          Lee-Ping

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