[gmx-users] Re[4]: g_msd vs g_velacc. [SOLVED]

Vitaly Chaban vvchaban at gmail.com
Mon Jun 16 10:57:09 CEST 2008

> I've got a discrepancy calculating the diffusion coefficient via
> Green-Kubo equation and via Einstein equation.

> $ g_velacc -nonormalize -acflen 1001
> $ g_analyze -f vac.xvg -integrate
> Do I miss any important keyword here? It seems the result of integration is not
> correct in this case.

For the VACF of the molecules:
$ g_velacc -nonormalize -acflen 1001 -mol -n index.ndx (index.ndx
contains the number of molecules for the calculation)

$ g_analyze -f vac.xvg -integrate

The result should be finally divided by 3.

Vitaly V. Chaban
School of Chemistry
University of Kharkiv
Svobody sq.,4
Kharkiv 61077, Ukraine

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