[gmx-users] [Fwd: Question re: GROMACS units]

David 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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