[gmx-users] cutt offs

[Ilya Chorny]

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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