[gmx-users] VAC

Eric Jakobsson jake at ncsa.uiuc.edu
Tue Jan 27 02:24:05 CET 2004

One thing to try with VAC's like water where oscillations are overlaid on 
relaxation is to Fourier analyze the VAC and subtract off the high 
frequency components, so you are left with some sort of smoothed 
relaxation, and also perhaps some insights from the Fourier distribution 
itself.  We did this some years ago for ions and water in gramicidin channel.

At 07:46 PM 1/21/2004 +0100, you wrote:
>It  might depend a bit on the type of VAC curve you are working with. For 
>the C-H vector relaxations the curve decays to an average value, and in 
>theory it should never be anti-correlated (i.e. below the long-time 
>average value).
>In that case there will only be a couple of negative points at long times, 
>so you can either use the absolute value after subtracting the baseline, 
>or drop points that are negative.
>Obviously, this won't work for something like the velocity autocorrelation 
>function of water molecules where you have anticorrelation for short 
>times. I don't have any immediate idea what to do there, but the log-log 
>plots are less interesting since it is a much more complicated relaxation 
>On Jan 21, 2004, at 6:34 PM, Lianqing Zheng wrote:
>>Hi, Erik:
>>I just read your article "molecular dynamics simulation of NMR relaxation
>>rates and slow dynamics in lipid bilayers" submitted to JCP in your phd
>>thesis, in which you discussed double-logarithmic plot of velocity
>>autocorrelation function. Hope you still remember it. :) It's quite
>>interesting to me since I'm trying to get some dynamical properties from
>>well-converged autocorrelation functions. I tried to plot double-log plots
>>of my ACFs, but immediately found a problem: some values in ACF are
>>negative, so there is no corresponding log values. What did you deal with
>>this problem?
>>PS: I don't know your personal email, so send this email to this list.
>>Hope this is OK. :)
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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