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*
>
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>
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue Aug 08 2017 - 10:30:02 PDT
