[gmx-users] cutt offs

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Mon Dec 29 19:27:00 CET 2003

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.


-----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 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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