On Wed, 2009-05-27 at 11:00 +0200, Yan Chai wrote: > If my understanding above is correct, it seems that the concept or > the algorithm of neighborlist for the twin range cut-off's in Gromacs > is different from the original concept of Verlet neighborlist which is > discussed in the textbook on MD simulations, for instance, in the book > Understanding Molecular Simulation by Frenkel and Smit. The original > algorithm of Verlet list needs rlist>rvdw in order to contain all > particles which might have interactions. However, the twin range > cut-off's in Gromacs with rvdw>=rlist seems to be contradict to this > original idea of Verlet list and to miss some contribution to the > interaction by the particles which stay between rlist and rvdw in the > normal steps without updating the neighborlist. > > So my question is: what is the idea for Gromacs to take such > algorithm of twin range cut-off's?
In the twin range method [1] interactions that are in the range rlist..rvdw are only calculated during neighborlist updates. In the mean time they are considered to stay constant. The idea behind this is that when r>rlist the interactions are weaker and also vary more slowly, thus one doesn't need to be as precise in taking those interactions into account. [1] http://dx.doi.org/10.1002/prot.340060203 -- ------------------------------------------------------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------------------------------------------------------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
