Re: [AMBER] tcorr and order parameters

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 15 Jun 2015 21:27:00 -0600

Hi Travis,

I'd have to re-visit the original paper by Prompers and Brüschweiler to be
certain, but I think the order parameter calculation only depends upon
diagonalizing the IRED matrix. The correlation functions are then used in
conjunction with that to get relaxation (T1/T2). So changing tcorr shouldnt
affect the order parameters.

-Dan

On Monday, June 15, 2015, Travis Hughes <THughes.scripps.edu> wrote:

> 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)
>
> Thanks,
> Travis
>
> Travis Hughes, PhD
> Kojetin Lab
> Molecular Therapeutics
> The Scripps Research Institute
> Jupiter, FL
>
>
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> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jun 15 2015 - 20:30:02 PDT
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