[gmx-users] cutt offs

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Mon Dec 29 22:21:01 CET 2003

Your example is extreme. What about the case of a single charge in
water. The water-water Coulomb cut off should be less than the charge
water Coulomb cutoff.


-----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 12:40 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] cutt offs

On Mon, 29 Dec 2003, Ilya Chorny 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.
That is an approximation, and since LJ potential goes to zero faster it 
can be justified (although that does not mean it is correct). 
Treating different parts of the system with different 
cut-off is worse. Let's say we divided a 6x6x6 nm system in two pieces, 
that with X coordinate < 3 nm and that with X > 3 nm. Now if we use a 
different cut-off for the first half of the system than for the other 
half, we create artifacts on the border between the two, and what's
I suspect that for such a system in "equilibrium" the chemical potential

is not the same in both halves. It will hence be impossible to define
kind of ensemble is modeled. Treating cut-offs differently for the
and water is the same kind of division, comparable in nature to 
simulations in implicit solvent. 

>>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).

And to come back to that simulation, they also determined solvation free

energies from that, but from just the protein coordinates, dismiising
all the 

Just my (possibly biased) opinion...

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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