For treatments that require a non-zero buffer length, like shift and switch, you do this by setting rlist larger than rcoulomb. Coulomb should be fine with PME + straight cutoff and the difference for LJ between nstlist=1 and nstlist=10 I expect will be negligible for a 2fs timestep. Note that I have never tried shifting or switching in gromacs, but charmm-like behaviour here seems 100% possible in gromacs.

Here is some stuff from the manual:
"The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rcoulomb to accommodate for the size of charge groups and diffusion between neighbor list updates." "The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list updates."

So yes, it is not possible to use a cutoff for coulombic and LJ while having nstlist>1 and obtaining results that are identical to those that would be obtained with nstlist=1 (or with sufficient 'buffer'). If you really must do this then set nstlist=1.

Chris.

-- original message --

Usually when we do neighbour searching we should give three parameters: cut-off distance, buffer length and the frequency of the neighbour list updating. But in Gromacs *.mdp file it's just required to give rlist,nstlist, rvdw and rcoumlomb. Where is the buffer length of neighbour searching in Gromacs?

_______________________________________________
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

Reply via email to