Re: [AMBER] Problems on IRED analyses for order parameter

From: Ye Wei <>
Date: Mon, 13 Jan 2014 12:29:30 +0800 (CST)

Hi Dac,

Thank you very much for your prompt reply and helpful suggestions.
I'm always misunderstanding on the tstep and tcorr, and confused on the relaxation rates and order parameters.
I will first try your recommendations and see if the problem is figured out.

It is the same, in your description, between Cpptraj and ptraj in only calculating the order parameters. Am I right?


At 2014-01-13 02:52:24,"David A Case" <> wrote:
>On Sun, Jan 12, 2014, Ye Wei wrote:
>> 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
>> vector v2 :2.N ired :2.H
>> vector v3 :3.N ired :3.H
>> ...
>> vector v126 :129.N ired :129.H
>Make sure you have exactly 126 vectors above; I don't know what is in the
>"...", but it looks like you have vectors v2 to v126, which would be 125.
>> 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
>> "
>> Some reference papers suggest the sampling time window should be 200 ps,
>> so I set tstep=200
>No: tstep should be the actual time step between your trajectory frames. It
>has nothing to do with what anything (including the "sampling time window")
>*should* be.
>> And the 100000.0 shows my MD traj is 100 ns' long.
>No: the tcorr time is the time over which to caclulated correlation functions,
>which should generally be much shorter than the length of the simulation.
>> I am so confused about the description about tstep and tcorr in
>> AmberTools Manual, what is their unit? [ps/ns]?
>You can choose what units you like, as long as tstep and tcorr are the same.
>(I'd use ps to be a little safer, however. Order parameters don't depend on
>the time unit, but things like relaxation rates do.)
>See the example/test calculations in
>.../hope this helps...dac
>AMBER mailing list

Wei Ye, PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science,
Shanghai Jiaotong University
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Received on Sun Jan 12 2014 - 21:00:02 PST
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