[AMBER] Problems on IRED analyses for order parameter

From: Ye Wei <yw20055968.126.com>
Date: Sun, 12 Jan 2014 22:37:33 +0800 (CST)

Dear Amber Users:
I am currently doing IRED analyses to calculate S2 (order parameters).
I am using Lysozyme as a test example.
Following is my Cpptraj Script:
trajin xxx.md.crd
vector v2 :2.N ired :2.H
vector v3 :3.N ired :3.H
vector v126 :129.N ired :129.H

matrix ired name matired order 2
diagmatrix matired vecs 126 out ired.vec name ired_vec
ired relax freq 500 order 2 tstep 200.0 tcorr 100000.0 out output.out noefile noe modes ired_vec
vector number is 126 because the first residue and two prolines don't have N-H relaxation order parameter.
Some reference papers suggest the sampling time window should be 200 ps, so I set tstep=200
And the 100000.0 shows my MD traj is 100 ns' long.
I am so confused about the description about tstep and tcorr in AmberTools Manual, what is their unit? [ps/ns]?
The results are very wired:
All the order parameters along sampling time decreased from about 20 to minus values (about -1.xx or -0.xxx or sth. else).
I don't know if there is something wrong through this work flow.
Of course, if I used ptraj to do following command:
vector v2 :2.N ired :2.H
vector v3 :3.N ired :3.H
vector v126 :129.N ired :129.H
matrix ired name matired order 2
analyze matrix matired vecs 126 out ired.vec order orderparamfile output.dat

A result that looks like right could be generated, but the sampling time and "sample from a plateau" that most papers said could not be conducted.
Has anyone ever met this situation? Or could anyone please help me to figure this out?
Many thanks
and Best Wishes,

Wei Ye, PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science,
Shanghai Jiaotong University,
Email: yw20055968.126.com
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Received on Sun Jan 12 2014 - 07:00:03 PST
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