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.
Mark
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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
