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.
PS:
It is the same, in your description, between Cpptraj and ptraj in only calculating the order parameters. Am I right?
Best,
Wei.
At 2014-01-13 02:52:24,"David A Case" <case.biomaps.rutgers.edu> 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 xxx.md.crd
>>
>> 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
>$AMBERHOME/AmberTools/test/cpptraj/Test_IRED.
>
>.../hope this helps...dac
>
>
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--
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 - 21:00:02 PST
