[gmx-users] g_msd vs g_velacc

Xavier Periole X.Periole at rug.nl
Sun Jun 15 11:43:16 CEST 2008

On Sun, 15 Jun 2008 12:17:01 +0300
  Vitaly Chaban <vvchaban at gmail.com> wrote:
> I've got a discrepancy calculating the diffusion coefficient via
> Green-Kubo equation and via Einstein equation.
>For methanol (200ps, dt=0.001):
> frequency to write velocities = 5
> frequency to write coordinates = 100
Any rationale behind this difference? That might well result in differences
of C(t) at short times.
> $ g_msd
> 2.3 (and it is true)
How much of msd(t) did you use? The part of the curve you use to fit
to Einstein equation will affect enormously the result!
> $ g_velacc -nonormalize -acflen 1001
> $ g_analyze -f vac.xvg -integrate
> 1.3 (and it's almost two times lower...)
Here you use 1001 points to integrate! Which result to 1001*0.005fs=5 ps!

Again did you use the same length of the msd(t) to fit via Einstein equation?

Although the difference in time scales you probably use might explain
the difference, that difference is actually small (same units?)!

> Do I miss any important keyword here? It seems the result of integration is 
> not correct in this case.
> Thanks,
> Vitaly V. Chaban
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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