[gmx-users] Scale down/ up velocities when coupling temperature and pressure?

[Erik Marklund]

I believe that it's all described with reasonable detail in the manual.

Erik

31 mar 2012 kl. 18.42 skrev Yun Shi:

> Hi all,
> 
> I am just wondering about how GROMACS works when coupling temperature and pressure.
> 
> Assuming the simplest coupling method, like Berendsen, does GROMACS just scale down/ up kinetic energy (KE) for each particle in the system, such as KE1/KE2 = T1/T2 ? Similarly for pressure, KE1/KE2 = P1/P2? So GROMACS scales the square root of velocities for every particle after each time step?
> 
> 
> -----------------------------------------------------------------
> BTW, the number of degrees of freedom = 3N - Nc - Ncom according to the manual. For conventional MD, is Nc equal to the total number of constrained bonds (like all bonds in gromos ff, and all bonds involving hydrogens in amber99sb ff)?
> 
> Thanks for any explanation.
> 
> Yun
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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