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.
--
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
