[AMBER] tcorr and order parameters

From: Travis Hughes <THughes.scripps.edu>
Date: Mon, 15 Jun 2015 19:08:30 -0400

Hi, I am doing protein methyl order parameter analysis of a trajectory for eventual comparison to NMR data. I run the following commands in cpptraj

parm myprotein.prmtop
trajin myprotein_002nw.nc
vector v0 .27 ired @29
vector v1 @95 ired @97
vector v2 .122 ired @124
vector v109 .4330 ired @4332
vector v110 .4384 ired @4387
vector v111 .4455 ired @4457
matrix ired name matired order 2
diagmatrix matired vecs 112 out ired.vec name ired.vec
ired tstep 20.0 tcorr 10000.0 out v0.out order 2 modes ired.vec orderparamfile 10ns.order

The orderparamfile that contains the order parameters seems to have reasonable values, however when I change tcorr to 40 or 100000000 (or anything that I have tried so far) the order parameter values stay exactly the same to the last digit.
It makes sense to me that the order parameters should depend on tcorr, but in this analysis they do not. Am I doing something wrong? (snapshots are saved to my trajectory file every 20ps my trajectory is 500ns long)


Travis Hughes, PhD
Kojetin Lab
Molecular Therapeutics
The Scripps Research Institute
Jupiter, FL

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Received on Mon Jun 15 2015 - 16:30:02 PDT
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