[gmx-users] VAC

Erik Lindahl lindahl at csb.stanford.edu
Wed Jan 21 19:48:01 CET 2004


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.



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. :)
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list