Thank you, Erik. Cheers.
Regards, Jian -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Erik Lindahl Sent: Friday, July 20, 2007 5:16 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FW: rvdw Hi Jian, The cutoff is based on the center of geometry of the "charge group" definitions in your topology. Since we typically use PME nowadays the don't have to be neutral, so "neighborsearching group" would probably be a better name. If each atom is a separate charge group the cutoff is thus based on their centers. Cheers, Erik On Jul 20, 2007, at 11:05 AM, Yin Jian wrote: > Thanks a lot, Hess. > By the way, what is the cutoff criteria used in Gromacs, is it > nonzero overlap between LJ-spheres or the mass-centers reside > in the LJ-sphere? Since these two are significantly different > in the dynamics way of cutoff. > I may take a look of the code ns.c. later. > > > Regards, > Jian > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:gmx-users- > [EMAIL PROTECTED] On Behalf Of Berk Hess > Sent: Friday, July 20, 2007 4:56 PM > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] FW: rvdw > > > > >> From: "Yin Jian" <[EMAIL PROTECTED]> >> Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >> Subject: RE: [gmx-users] FW: rvdw >> Date: Fri, 20 Jul 2007 16:40:09 +0800 >> >> Hi Hess, >> Thanks for your comments, although we have difference in this >> topic. The carrier of depletion force at least for me is >> not sure. So we want to do a test anyway in this way. >> >> >> >> Regards, >> Jian > > Ah, now I understand what you want to do. > > For that it would help to have different cut-offs. > We are (currently) not going to implement such a thing. > But is should not be too difficult to modify the cut-off > check for the neighborlist in ns.c. > > Berk. > > _________________________________________________________________ > Need a brain boost? Recharge with a stimulating game. Play now! > http://club.live.com/home.aspx?icid=club_hotmailtextlink1 > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
