[gmx-developers] 4.6b1 cutoff-scheme=verlet + vdw/coulombtype=User

[Anton Feenstra]

On 05/12/12 15:53, Mirco Wahab wrote:
> Am 05.12.2012 14:26, wrote Berk Hess:
>> User tables are not supported with the Verlet scheme in 4.6.
>> We plan to support this in 5.0.
>> What do you want to use the tables for?
>
> For example: by constructing a non-bonded interaction
> potential (implicit solvent) in the spirit of Markus
> Deserno's WCA/Cos² potential (Espresso Package) and
> re-parameterizing Sievert Marrinks coarse-grained Lipids
> to this water-free concept, one can abuse Gromacs to do
> interesting simulations on very large systems.
>
> BTW. there would be some other nice things to have in
> later versions:
>
> - simpler "freeze groups",
>    completely exclude/ignore molecules or parts
>    of molecules from the integrator
>
> - atoms/groups combined to rigid-bodies
>    and integrated as a whole (rigid-body mechanics)

With some (possibly a lot) of work, you could do the following:
- construct a tetrahedron of four particles that reproduces the total 
mass and moments of inertia of your rigid body of interest. These 
particles will have mass, but no interaction.
- create virtual site (a.k.a. 'dummy atoms') constructions from the four 
mass-particles for each atom in your rigid body. THese virtual atoms 
will have interactions (LJ, Coul), but no mass.

This would be along the same lines as the virtual site constructions for 
explicit hydrogens and for planar sidechains that Berk and me did a long 
time ago: /J. Comput. Chem./ 1999, *20*, 786-798.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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