[gmx-users] Re[2]: g_msd vs g_velacc

[Xavier Periole]

On Sun, 15 Jun 2008 19:07:48 +0300
  Vitaly Chaban <vvchaban at gmail.com> wrote:
>>>For methanol (200ps, dt=0.001):
>>> frequency to write velocities = 5
>>> frequency to write coordinates = 100
> XP> Any rationale behind this difference? That might well result in 
> differences of C(t) at short times.
> 
> Yes, the difference is dictated by the pure logic.
That is a clear explanation! Thank you.
>>> $ g_msd
>>> 2.3 (and it is true)
> XP> How much of msd(t) did you use? The part of the curve you use to fit
> XP> to Einstein equation will affect enormously the result!
> 
> 200 ps of trajectory was used. It is quite enough.
It depends on many factors: the length of your simulation and the
convergence of your msd curve are two of them.
> XP> Here you use 1001 points to integrate! Which result to 1001*0.005fs=5 ps!
I tried to determine the length of your velocity C(t) you used to extract
the correlation time.

It seems that you used 5 ps for the velocities and 200 ps for the msd!
That might be a reason fot differences, no?
> XP> Again did you use the same length of the msd(t) to fit via Einstein 
> equation?
> 
> Sorry, there is no sense in what you say here.
> 
> 
> 
> 
> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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