[gmx-users] Heating schemes
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 29 08:46:34 CEST 2006
Mark Abraham wrote:
> Hi all,
> MD protocols in papers show a wide variety of heating schemes, including
> heating from zero K in stepwise fashion with a certain amount of MD time
> at various temperatures, and just jumping straight in the deep end at
> the simulation temperature and running for a while to hopefully enter
> the equilibrated region of phase space.
> While I can see the intellectual attraction of a gradual heating scheme,
> the chaotic nature of the integrators makes me suspect that it doesn't
> make much of an impact. Is anybody aware of meaningful differences
> induced by these schemes? Are there any published studies comparing them?
I'm not aware of any. Obviously you want an equilibrated starting
structure, but close to the original one. This is why we usually propose
to use position restraints initially, such that energy and density can
relax before releasing the protein.
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David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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