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

Erik Marklund erikm at xray.bmc.uu.se
Sat Mar 31 21:16:29 CEST 2012

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


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
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120331/27f9276d/attachment.html>

More information about the gromacs.org_gmx-users mailing list