[gmx-users] VAC

[Lianqing Zheng]

Thanks, Eric! Could you introduce me any references where I can find the
details of this method? Thanks.

Lianqing


On Sun, 25 Jan 2004, Eric Jakobsson wrote:

>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.
>Eric
>
>At 07:46 PM 1/21/2004 +0100, you wrote:
>>Hi,
>>
>>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 
>>process.
>>
>>Cheers,
>>
>>Erik
>>
>>
>>
>>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?
>>>
>>>Thanks!
>>>
>>>Lianqing
>>>
>>>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 
>Biochemistry
>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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