[gmx-users] [Fwd: Question re: GROMACS units]
spoel at xray.bmc.uu.se
Thu Jun 9 20:16:12 CEST 2005
Dear GROMACS Community,
This program is fantastic.
I have a question regarding rescaling units. I'm using the Brownian
Dynamics integrator option of mdrun to do a Brownian dynamics
simulation of colloidal particle interactions. These particles are
around .7 microns, uncharged, and at room temperature. I'm only
simulating one type of particle.
Question: If my input files (table.xvg, md.mdp, etc) to the Gromacs
simulation are set up so that the particle radius is ".7" (e.g., the
table.xvg potential has a minimum at 1.4) -- so that my length scale
is now in microns, rather than the usual nanometers -- and as long as
my particles are uncharged -- can I safely interpret all the output
values from the simulation in an appropriately rescaled manner?
More to the point -- if I consider my length scale to be microns
rather than nanometers, can I easily determine the units of energy
for the potential in table.xvg? What are units of temperature?
It is described in the manual, chapter 2. In cannot really describe it any better.
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://xray.bmc.uu.se/~spoel
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