Hi, Feng,
Yes, I realize it and already re-run the job.
Thanks,
Best,
*Chunli*
On Tue, Aug 8, 2017 at 1:27 PM, Feng Pan <fpan3.ncsu.edu> wrote:
> Hi, Chunli
>
> First, it seems that you use the wrong value for the anchor_position. Here
> all the values should be
> in radians, but seems you use degrees. So you need to change to radians
> first.
>
> To draw the path, use the reparametrized centers of different images in the
> mdout file.
>
> Feng
>
> On Mon, Aug 7, 2017 at 9:49 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
>
> > Hello,
> >
> > In the string methods, what does it means in the stsm.001.out file below:
> >
> > # = NFE%STSM Initial
> > Pathway==================================================
> >
> > # << anchor(1) : position = 3.960000, strength = 20.000000 >>
> >
> > # << anchor(2) : position = -130.020000, strength = 20.000000 >>
> >
> > #
> > ------------------------------------------------------------
> > -----------------
> >
> > # MD time (ps), CV(1:2)
> >
> > #
> > ============================================================
> > =================
> >
> > 0.0000 0.06914130 -2.26923847
> >
> > 0.0200 0.07271208 -2.73408209
> >
> > 0.0400 0.07652805 -2.84965414
> >
> > 0.0600 0.07795472 3.03822033
> >
> > 0.0800 0.08241867 3.12142878
> >
> > 0.1000 0.08495199 3.01791427
> >
> > 0.1200 0.08555569 2.86717038
> >
> >
> > .....
> >
> >
> >
> > and
> >
> >
> > NFE : # << colvar(1) = 0.007826 0.022057 >>
> >
> > NFE : # << colvar(2) = -2.694593 -2.964593 >>
> >
> > NFE : # drifted center of image 1 : 40 0.00782640
> > -2.69459250
> >
> > NFE : # drifted center of image 2 : 40 0.52288431
> > 0.91052733
> >
> > NFE : # drifted center of image 3 : 40 2.56373851
> > 0.70046240
> >
> > NFE : # drifted center of image 4 : 40 0.07509091
> > -2.20667518
> >
> > NFE : # drifted center of image 5 : 40 0.89524373
> > -0.76143378
> >
> > NFE : # smoothed center of image 1 : 40 0.00782640
> > -2.69459250
> >
> > NFE : # smoothed center of image 2 : 40 0.57346627
> > 0.89674353
> >
> > NFE : # smoothed center of image 3 : 40 2.51138799
> > 0.64872570
> >
> > NFE : # smoothed center of image 4 : 40 0.06100224
> > -2.15863523
> >
> > NFE : # smoothed center of image 5 : 40 0.88727440
> > -0.70817694
> >
> > NFE : # smoothed center of image 6 : 40 0.72381698
> > -2.91261127
> >
> >
> > NFE : # reparametrized center of image 1 : 40 0.00782640
> > -2.69459250
> >
> > NFE : # reparametrized center of image 2 : 40
> 0.42696645
> > 1.12313090
> >
> > NFE : # reparametrized center of image 3 : 40
> 1.98923377
> > 0.73173851
> >
> > NFE : # reparametrized center of image 4 : 40
> 1.92101428
> > 0.24929126
> >
> > NFE : # reparametrized center of image 5 : 40
> 0.12852031
> > -2.12319703
> >
> > NFE : # reparametrized center of image 6 : 40
> 0.88562494
> > -0.71647809
> >
> > which one do I use to get the attached plot?
> >
> > Below is my colvar file:
> >
> > cv_file
> >
> > &colvar ! Pseudo-dihedral
> >
> > cv_type = 'COM_TORSION'
> >
> > cv_ni = 57, cv_i =
> > 138,139,141,143,144,147,148,149,200,201,203,204,205,206,
> > 209,210,212,213,422,423,425,426,430,431,432,434,435,486,
> > 487,489,490,491,492,493,495,496,499,500,0,156,157,158,0,
> > 188,189,190,0,168,169,171,172,176,177,178,180,181,0
> >
> > anchor_position = 3.96
> >
> > anchor_strength = 20.0
> >
> > /
> >
> > &colvar ! Glycosidic torsion
> >
> > cv_type = 'TORSION'
> >
> > cv_ni = 4, cv_i = 180, 168, 166, 165
> >
> > anchor_position = -130.02
> >
> > anchor_strength = 20.0
> >
> > /
> >
> > Best,
> >
> >
> > *Chunli*
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
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>
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Received on Tue Aug 08 2017 - 11:00:02 PDT
