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.
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