[gmx-users] how to do simulation at high temperature
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 9 12:11:58 CEST 2006
Nguyen Hoang Phuong wrote:
>>That is the same as reducing the timestep!
> not really. If one runs simulations at high temperature with the
> original mass then the kinetic energy becomes very high--> simulations
> maybe crashed. By increasing mass then the kinetic energy is reduced and
> the simulations are more stable. Check: Proteins 25, 79-88 (1996)
That paper is not correct. First, they increase the masses by a factor
w, which means that Ekin is also larger by a factor w. That means that
any motion is reduced in speed by a factor of 1/sqrt(w). In addition, to
maintain stability the timestep has to be reduced by a factor of
1/sqrt(w). Anyway, if it worked then we would all simulate our molecules
with the mass of the sun...
You may want to check:
Title: Improving efficiency of large time-scale molecular dynamics
simulations of hydrogen-rich systems
Author(s): Feenstra KA, Hess B, Berendsen HJC
Source: JOURNAL OF COMPUTATIONAL CHEMISTRY 20 (8): 786-798 JUN 1999
Document Type: Article
Cited References: 34 Times Cited: 85 Find Related Records
Abstract: A systematic analysis is performed on the effectiveness of
removing degrees of freedom from hydrogen atoms and/or increasing
hydrogen masses to increase the efficiency of molecular dynamics
simulations of hydrogen-rich systems such as proteins in water. In
proteins, high-frequency bond-angle vibrations involving hydrogen atoms
limit the time step to 3 fs, which is already a factor of 1.5 beyond the
commonly used time step of 2 fs. Removing these degrees of freedom from
the system by constructing hydrogen atoms as dummy atoms, allows the
time step to be increased to 7 fs, a factor of 3.5 compared with 2 fs.
Additionally, a gain in simulation stability can be achieved by
increasing the masses of hydrogen atoms with remaining degrees of
freedom from 1 to 4 u. Increasing hydrogen mass without removing the
high-frequency degrees of freedom allows the time step to be increased
only to 4 fs, a factor of two, compared with 2 fs. The net gain in
efficiency of sampling configurational space may be up to 15% lower than
expected from the increase in time step due to the increase in viscosity
and decrease in diffusion constant. In principle, introducing dummy
atoms and increasing hydrogen mass do not influence thermodynamical
properties of the system and dynamical properties are shown to be
influenced only to a moderate degree. Comparing the maximum time step
attainable with these methods (7 fs) to the time step of 2 fs that is
routinely used in simulation, and taking into account the increase in
viscosity and decrease in diffusion constant, we can say that a net gain
in simulation efficiency of a factor of 3 to 3.5 can be achieved. (C)
1999 John Wiley & Sons, Inc.
>>Check chapter 2 of the manual about units...
>>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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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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