[gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb
erikm at xray.bmc.uu.se
Fri Feb 11 14:41:05 CET 2011
Mark Abraham skrev 2011-02-11 14.17:
>> I am a user of gromacs. I am quite confused when I came across the
>> relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.
>> In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
>> in switch/shift, it says rvdw should be smaller than rlist...
>> I guess in cut-off, it's to get all the updated atoms in the calculation
>> of vdw/ coulomb by setting rvdw/ rcoulomb greater, but why it's the
>> opposite in switch...
>> Could you help me to understand how it's done? Thanks a lot.
> They're different algorithms, and they work as described. rlist
> controls the size of the neighbour lists, which list all the atom
> pairs whose interactions the nonbonded kernels compute each MD step.
> rvdw/rcoulomb control where the interaction is judged to be small
> enough that particles at greater distances can be neglected. The only
> basis governing their relative size is the algorithm you want to
> implement. With twin-range neighbourlists, the interactions between
> rvdw and rcoulomb and rlist are computed whenever the neighbour lists
> are constructed, and re-used for nstlist steps (see manual 3.4.2).
> With switch/shift interactions, GROMACS generates the potential in
> tabular form, so that if rlist > rvdw, then some interactions will be
> computed at distances such that the resulting potential will be known
> to be zero (see manual 4.1.5). In both cases there's a trade-off
> between the cost of re-constructing the neighbour lists, the cost of
> evaluating the resulting interactions and the accuracy limitations
> imposed by the underlying assumptions.
And if I'm not mistaken (if I am, please do correct me) the reason for
having rlist > rvdw with shift/switch is that the neighbourlists are
made based on charge group distance rather than atomic distances. Hence
there may be atoms closer than rvdw in the neighbourlists although the
centers of their respective chargegroups are separated by more than rvdw.
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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