On Wed, Apr 27, 2016, Saheb Dutta wrote:
> We attempt to calculatethe time correlation function using amber11
> (auto time-correlation function (tcf)of the N-H vector) for a protein
> molecule. We have the total trajectory dividedinto 44 mdcrd files
> of various time spans (such as 100 ps, 150 ps and 200 ps)for a
> total 6 ns trajectory length. Time step is 0.1 ps for each frame
> withinall mdcrd files. The problem is the calculated tcf exhibits a
> sudden riseat the time step corresponding to the beginning of the
> next mdcrd file. Forexample, the tcf decays from 1 in the first
> trajectory which ends at a value of0.8614 at 149.9 ps. However, the
> tcf value at 150 ps is 0.8734 at the start ofthe next mdcrd file and
> decays subsequently. Again, the value suddenly rises atthe time step
> corresponding to the beginning of the next mdcrd file.Consequently, the
> tcf plot exhibits spike like features through out its decay. The ptraj
> script used is appended below.
Dan's question about irest is relevant, but you might also see this behavior
if you used a Langevin thermostat and did not set ig=1 (or otherwise make sure
to get a new random number at beginning of each section of the trajectory.)
Apologies if this is not the problem: to be sure, when calculating time
correlation functions, you should be using NVE conditions (no thermostat),
since all thermostats muck with dynamical behavior.
...dac
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Received on Wed Apr 27 2016 - 18:30:03 PDT
