[gmx-developers] vdW-tabulated potential in charge-group kernel

Berk Hess hess at kth.se
Mon Nov 24 10:20:20 CET 2014


Apart from the coefficient scaling, the electrostatics and VdW tables 
have been combined. That should be easy to figure out by looking at 
nb_generic.c. The stride of VFtab is now 12, the dispersion is now in 
entries 4-7 and the repulsion in entries 8-11.



On 11/24/2014 10:10 AM, Tristan Bereau wrote:
> Dear all,
> I've been toying with the charge-group kernel
> (gmxlib/nonbonded/nb_generic_cg.c) as a means to easily implement a
> somewhat exotic interaction potential. That implementation runs well in
> Gromacs 4.5.4.
> Since that, I've tried porting it to 4.6.6. I've found inconsistencies
> between the two versions affecting the vdw-tabulated potentials:
> - the C6 and C12 coefficients (in the vdwparam array) differ by a factor
> of 6 and 12, respectively.
> - the vdW tables (previously nblists->vdwtab, now
> kernel_data->table_elec_vdw->data) are now very different--I can't tell
> what's the relationship between the old and new ones, unfortunately.
> As a result, the exact same simulation using a vdW-tabulated force field
> with gromacs 4.5.4 and 4.6.6 yield very different energies. Has there
> been a change in convention in the input force field for the
> charge-group kernel? There seems to be an inconsistency somewhere.
> Many thanks for your help.
> Best,
> Tristan

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