By the way, I was using radians in colvar file not degree:
cv_file
&colvar ! Pseudo-dihedral
cv_type = 'COM_TORSION'
cv_ni = 29, cv_i =
200,201,203,204,205,206,209,210,212,213,0,156,157,158,0,188,189,190,0,168,169,171,172,176,177,178,180,181,0
anchor_position = -0.401
anchor_strength = 20.0
/
&colvar ! Glycosidic torsion
cv_type = 'TORSION'
cv_ni = 4, cv_i = 180, 168, 166, 165
anchor_position = -2.269
anchor_strength = 20.0
/
Best,
*Chunli*
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
>>
>
>
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Received on Thu Aug 17 2017 - 19:30:03 PDT
