Hi,
> 1) In the 2011 paper it is said that a typicall value for the
> autocorrelation time is something in the range of 1 ps but in my
> calculations (about 2 ns length) my autocorrelation times are really
> larger than that value. I am using samplings of 1 conformation/ps and 100
> conformations/ps and in both cases the autocorelation times range roughly
> from 10ps to 200ps (see attached text file). I am using timespets of 1 fs
> and langevin thermostat (ntt=3) with gamma_ln=2. Does it make any sense?
I think the number given is specific to the system and TI setup used
there. For small, rigid molecules in water, autocorrelation times are
quite small, dvdl-series look more or less like white noise. I would not
be suprised if different molecules and different transformations gave
quite longer autocorrelation times.
If you want to compare your script to other software, you could just use
xmgrace or origin on one example dvdl-time series.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jun 27 2013 - 10:30:02 PDT
