[gmx-users] FW: rvdw

[Erik Lindahl]

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: gmx-users-bounces at gromacs.org [mailto:gmx-users- 
> bounces at gromacs.org] On Behalf Of Berk Hess
> Sent: Friday, July 20, 2007 4:56 PM
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] FW: rvdw
>
>
>
>
>> From: "Yin Jian" <smayinj at nus.edu.sg>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: "Discussion list for GROMACS users" <gmx-users at 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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