Re: [AMBER] tcorr and order parameters

From: Travis Hughes <THughes.scripps.edu>
Date: Tue, 16 Jun 2015 15:49:48 -0400

Dan,
That is good news, I will have to look at that paper also.
Thanks
Travis

Travis Hughes, PhD
Kojetin Lab
Molecular Therapeutics
The Scripps Research Institute
Jupiter, FL


> On Jun 15, 2015, at 9:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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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>
>
> --
> -------------------------
> 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/
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Received on Tue Jun 16 2015 - 13:00:03 PDT
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