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

[Anton Feenstra]

David wrote:

>         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?

Yes.

>         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?

Read 'micrometer' in stead of 'nm' everywhere...!

Temperature is K. Simple.

There is only one exception for the pressure. There is the 'Wilfred' 
correction factor in it for 'energy density' (kJ mol^-1 nm^-3) to Bar
(it is about 16). That will get skewed a factor 10^9 if you use microns...

> It is described in the manual, chapter 2. In cannot really describe it any better.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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