[gmx-users] cutt offs

[Eric Jakobsson]

LJ and Coul have intrinsically different fall-off rates (square vs. 6th 
power) so there is a logic to saying that there is a difference in the 
distance beyond which they are negligible.  There is no physical logic to 
saying that the interaction energy between two charges depends on what kind 
of molecule they are in.

At 10:25 AM 12/29/2003 -0800, you wrote:
>Its not obvious to me why the thermodynamics would get screwed up. Its
>intuitively the same as having different cut offs for LJ vs Coul.
>
>Ilya
>
>-----Original Message-----
>From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
>On Behalf Of David van der Spoel
>Sent: Monday, December 29, 2003 10:14 AM
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] cutt offs
>
>On Mon, 29 Dec 2003, Eric Jakobsson wrote:
>
> >You would not want to do that anyway--it would really put you in
> >thermodynamic neverland.
>I agree, but IIRC this is what Amber does quite frequently, no cut-off
>within the protein, and short cut-off for protein-water and water-water
>(e.g. the 1 us folding sim of Duan and Kollman).
>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596,          75124 Uppsala, Sweden
>phone:  46 18 471 4205          fax: 46 18 511 755
>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)