[gmx-users] Re: g_velacc

rams rams rams.crux at gmail.com
Sun Aug 31 20:18:58 CEST 2008

How to monitor the motion of center of mass of a protein as it is the case
all the time to monitor this during the calculations of diffusion and
correlation functions. How far the values will be different if we monitor
the motion of backbone atoms rather than the center of mass motion.

I still dont have any idea how to get the diffusion constant using g_velacc.


On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban <chaban at univer.kharkov.ua>wrote:

> > No special reason, just mundane ones: computing the diffusion constant
> > through mean square displacement is easier in terms of convergence.
> But it is not applicable in the anisotropic systems, for example in
> ones with spatial confinements present... :)
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq.,4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
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