[AMBER] results for string methods

From: Chunli Yan <utchunliyan.gmail.com>
Date: Mon, 7 Aug 2017 21:49:45 -0400

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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Screenshot_2017-08-07_21.47.58.png
(image/png attachment: Screenshot_2017-08-07_21.47.58.png)

Received on Mon Aug 07 2017 - 19:00:02 PDT
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