Hi, Chunli
Since the torsion angle is periodic in [-3.14,3.14], if you add a 2*3.14 to
those negative numbers,
so curve will not look so weird.
But as I see, the path is not converged since the paths last several
repeats do not override with
each other. As I am afraid the COM torsion may may not describe the
flipping well as Carlos said.
Feng
On Fri, Aug 18, 2017 at 11:43 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
> Thanks, Carlos, I will read these papers.
>
> On Aug 18, 2017 3:41 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
> wrote:
>
> this isn't really directly related to your question, but for defining the
> base flipping center of mass groups you might want to read the following
> article where we examined the approach you are using and found
> difficulties, at least for our systems.
>
> An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
> Song, K., Campbell, A., Bergonzo, C., de los Santos, C., Grollman, A.,
> Simmerling, C.
> Journal of Chemical Theory and Computation, 2009, 5 (11), 3105-3113
> DOI: 10.1021/ct9001575
>
> for obtaining free energy profiles of flipping, including 2D mapping with
> the glycosidic angle, you could look at these examples:
>
> Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase
> Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
> C., Journal of the American Chemical Society, 2011, 133, 14504–14506
> DOI: 10.1021/ja205142d
>
> Active destabilization of base pairs by a DNA glycosylase wedge initiates
> damage recognition
> Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V.,
> de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O.,
> Simmerling, C., Nucleic Acids Research, 2015, 43 (1), 272-281
> DOI: 10.1093/nar/gku1300
>
> A Dynamic Checkpoint in Oxidative Lesion Discrimination by
> Formamidopyrimidine–DNA Glycosylase
> Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los
> Santos, C., Zharkov, D., Simmerling, C., Nucleic Acids Research,
> 2015,44(2), 683-94
> DOI:10.1093/nar/gkv1092
>
> DNA Deformation-Coupled Recognition of 8‑Oxoguanine: Conformational Kinetic
> Gating in Human DNA Glycosylase
> Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman,
> Dmitry O. Zharkov, and Carlos Simmerling, Journal of the American Chemical
> Society, 2017, 139 (7), 2682-2692
> DOI: 10.1021/jacs.6b11433
>
>
> On Thu, Aug 17, 2017 at 10:22 PM, Chunli Yan <utchunliyan.gmail.com>
> wrote:
>
> > Hi, Feng,
> >
> > I defined two colvars: Pseudo-torsion and Glycosidic torsion to find path
> > for base flipping in DNA. My initial centers are the following:
> >
> > Frame Pseudo #Frame Glycosidic
> >
> > 1 -22.9834 1 -130.0178
> >
> > 2 -1.8113 2 -105.8328
> >
> > 3 17.1431 3 -87.6128
> >
> > 4 18.1844 4 -59.2702
> >
> > 5 28.7286 5 -113.0601
> >
> > 6 37.1831 6 -123.4999
> >
> > 7 48.8440 7 -108.6611
> >
> > 8 60.1785 8 -151.3533
> >
> > 9 66.9365 9 -120.1098
> >
> > 10 68.9553 10 -137.1430
> >
> > 11 81.9498 11 -118.3375
> >
> > 12 122.5714 12 -154.9839
> >
> > 13 127.7331 13 -132.3430
> >
> > 14 145.1492 14 -146.8632
> >
> > 15 125.7844 15 -112.9243
> >
> > 16 144.7185 16 -134.7721
> >
> > 17 153.0255 17 -146.5084
> >
> > 18 167.3042 18 -127.8211
> >
> > 19 175.7482 19 -139.4776
> >
> > 20 179.6935 20 61.0230
> >
> > But after I simulate it using string methods, I have 20 images, 20
> repeats
> > per image and 300 iterations per repeats. I found some values changed
> from
> > positive to negative, such as the first iterations below:
> >
> > center of image 1 : 20 -0.40085575 -2.39713917
> >
> > center of image 2 : 20 -0.04998067 -1.95821022
> >
> > center of image 3 : 20 0.12711176 -1.43258465
> >
> > center of image 4 : 20 0.22593965 -1.67138273
> >
> > center of image 5 : 20 0.46420370 -2.12574684
> >
> > center of image 6 : 20 0.82577461 -2.03805261
> >
> > center of image 7 : 20 1.16971343 -2.49178907
> >
> > center of image 8 : 20 1.24398057 -2.30938805
> >
> > center of image 9 : 20 1.65712794 -2.21598440
> >
> > center of image 10 : 20 2.08806127 -2.58816551
> >
> > center of image 11 : 20 2.30771252 -2.34113196
> >
> > center of image 12 : 20 2.14452605 -2.12182890
> >
> > center of image 13 : 20 2.50822092 -2.44579490
> >
> > center of image 14 : 20 2.82097066 -2.25111436
> >
> > center of image 15 : 20 -3.03275023 -2.29560698
> >
> > center of image 16 : 20 -3.05625542 -2.37193291
> >
> > center of image 17 : 20 -3.07979668 -2.77849152
> >
> > center of image 18 : 20 -3.10334797 1.34943046
> >
> > center of image 19 : 20 -3.12688318 1.11151901
> >
> > center of image 20 : 20 3.13280899 1.05163244
> >
> > Please find attached two torsions I defined and final string plot.
> >
> >
> >
> > Best,
> >
> >
> > *Chunli*
> >
> >
> >
> > On Thu, Aug 17, 2017 at 6:48 PM, Feng Pan <fpan3.ncsu.edu> wrote:
> >
> > > Hi, Chunli
> > >
> > > String method can only give the least free energy path in the phase
> > space,
> > > cannot
> > > give the whole landscape of free energy.
> > >
> > > To get the PMF, you can use umbrella sampling, or the ABMD method by
> > &abmd
> > > module,
> > > you can check the manual for details.
> > >
> > > Best
> > > Feng
> > >
> > > On Thu, Aug 17, 2017 at 1:42 AM, Chunli Yan <utchunliyan.gmail.com>
> > wrote:
> > >
> > > > Hello,
> > > >
> > > > After I finished the simulation by using string methods, I got a
> lists
> > of
> > > > output file for each image (mdcrd*, rst*, stsm* and so on). In amber
> > > > manual:
> > > >
> > > > When you get the biasing potential (*.nc file), you can always use
> > the
> > > > nfe-umbrella-slice utility to access
> > > >
> > > > its content and get a friendly-written ASCII file from which one can
> > > obtain
> > > > the free energy map. The output
> > > >
> > > > is the free energy value, which is the opposite of the biasing
> > potential
> > > (
> > > > f = U (units kcal*=*mol )). The
> > > >
> > > > nfe-umbrella-slice utility has been included in AmberTools.
> > > >
> > > >
> > > > Usage: nfe-umbrella-slice [options] bias_potential.nc
> > > >
> > > >
> > > > I am wondering how to compute free energy along the image. How to get
> > the
> > > > biasing potential.
> > > >
> > > >
> > > > Thanks,
> > > >
> > > >
> > > > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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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 Sat Aug 19 2017 - 00:30:03 PDT
