[gmx-users] cutt offs
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 29 21:41:01 CET 2003
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 more,
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 what
kind of ensemble is modeled. Treating cut-offs differently for the protein
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
>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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