How to calculate Global Elasticity?
To calculate global elasticity, dnaMD globalElasticity command can be used. However, it takes HDF5 file as input. Following steps can be performed to generate HDF5 files. The tutorial file can be downloaded here. We will prepare HDF5 file for both free and bound DNA.
Calculate stretching twisting and bending motions
Both free and bound DNA is superimposed on to the same DNA structure. Careful that bending calculation is fitting dependent. Therefore, at first we aligned both free and bound DNA to a common DNA structure as follows
[ ]:
%%bash
# Align bound DNA
echo 6 0 | gmx trjconv -f inputs/F1_complex_DNA.xtc -s inputs/dna.tpr -n inputs/dna.ndx -o complex_dna_aligned.xtc -fit rot+trans
# Align free DNA
echo 6 0 | gmx trjconv -f inputs/F1_free_DNA.xtc -s inputs/dna.tpr -n inputs/dna.ndx -o free_dna_aligned.xtc -fit rot+trans
1. Run do_x3dna on DNA trajectory, -nofit is used because DNA is already superimposed to a common DNA structure using trjconv.
[ ]:
%%bash
# For free DNA
echo 2 | do_x3dna -f free_dna_aligned.xtc -s inputs/dna.tpr -n inputs/dna.ndx -ref -noavg -nofit -name free
mv *_free.dat outputs/.
# For bound DNA
echo 2 | do_x3dna -f complex_dna_aligned.xtc -s inputs/dna.tpr -n inputs/dna.ndx -ref -noavg -nofit -name bound
mv *_bound.dat outputs/.
2. Run dnaMD to extract the parameters from do_x3dna output files and save as HDF5 file. Also calculate global axis, curvature and tangents.
[8]:
%%bash
# For free DNA
dnaMD saveAsH5 -tbp 27 -i outputs/L-BPS_free.dat,outputs/L-BPH_free.dat,outputs/HelAxis_free.dat -o free_dna.h5
dnaMD axisCurv -tbp 27 -bs 2 -be 25 -ctan -scp 100 -s 1000 -cta 30 -io free_dna.h5 -ap free_dna_axis.pdb
# For bound DNA
dnaMD saveAsH5 -tbp 27 -i outputs/L-BPS_bound.dat,outputs/L-BPH_bound.dat,outputs/HelAxis_bound.dat -o bound_dna.h5
dnaMD axisCurv -tbp 27 -bs 2 -be 25 -ctan -scp 100 -s 1000 -cta 30 -io bound_dna.h5 -ap bound_dna_axis.pdb
Loading parameters: ['shift', 'slide', 'rise', 'tilt', 'roll', 'twist']
Reading file : L-BPS_free.dat
Reading frame 5000
Finished reading.... Total number of frame read = 5001
Loading parameters: ['x-disp', 'y-disp', 'h-rise', 'inclination', 'tip', 'h-twist']
Reading file : L-BPH_free.dat
Reading frame 5000
Finished reading.... Total number of frame read = 5001
Loading parameters: ['helical x-axis', 'helical y-axis', 'helical z-axis']
Reading file : HelAxis_free.dat
Reading frame 5000
Finished reading.... Total number of frame read = 5001
Fitting spline curve on helical axis of frame 5000 out of 5001 frames
Finished spline curve fitting...
... Calculating curvature and tangents
... Finished
Loading parameters: ['shift', 'slide', 'rise', 'tilt', 'roll', 'twist']
Reading file : L-BPS_bound.dat
Reading frame 10000
Finished reading.... Total number of frame read = 12001
Loading parameters: ['x-disp', 'y-disp', 'h-rise', 'inclination', 'tip', 'h-twist']
Reading file : L-BPH_bound.dat
Reading frame 10000
Finished reading.... Total number of frame read = 12001
Loading parameters: ['helical x-axis', 'helical y-axis', 'helical z-axis']
Reading file : HelAxis_bound.dat
Reading frame 10000
Finished reading.... Total number of frame read = 12001
Fitting spline curve on helical axis of frame 12000 out of 12001 frames
Finished spline curve fitting...
... Calculating curvature and tangents
... Finished
Now, we have HDF5 files of both free and bounds DNA. It can be used for the calculation of elastic properties. These files can be used with either dnaMD Python module or dnaMD globalElasticity.
Bending Stretching Twist Modulus
Following command calculate Bending Stretching Twist modulus matrix. Output matrix will be stored in csv file. Elastic modulus matrix is printed as output and average values of contour length and cumulative twist angle is also printed.
[1]:
%%bash
dnaMD globalElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 20 -estype BST -paxis X -o elastic_modulus_BST.csv
=========== Elastic Modulus Matrix ===========
337.233 28.506 -6.984 -20.710
28.506 373.863 7.977 39.509
-6.984 7.977 1080.722 -96.198
-20.710 39.509 -96.198 448.349
=========== ====================== ===========
========================= Average Values ==========================
Bending-1 Angle Bending-2 Angle Contour Length Sum. Twist
0.021 0.068 5.358 9.543
=========== ====================== ====================== ===========
The above modulus matrix is in this form:
Where:
\(M_{Bx}\) - Bending-1 stiffness in one plane
\(M_{By}\) - Bending-2 stiffness in another orthogonal plane
\(M_{S}\) - Stretch Modulus
\(M_{T}\) - Twist rigidity
\(M_{Bx,By}\) - Bending-1 and Bending-2 coupling
\(M_{By,S}\) - Bending-2 and stretching coupling
\(M_{S,T}\) - Stretching Twsiting coupling
\(M_{Bx,S}\) - Bending-1 Stretching coupling
\(M_{By,T}\) - Bending-2 Twisting coupling
\(M_{Bx,T}\) - Bending-1 Twisting coupling
Stretching Twist Modulus
Following command calculate Bending Stretching Twist modulus matrix. Output matrix will be stored in csv file. Elastic modulus matrix is printed as output and average values of contour length and cumulative twist angle is also printed.
[2]:
%%bash
dnaMD globalElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 20 -estype ST -o elastic_modulus_ST.csv
=========== Elastic Modulus Matrix ===========
1080.380 -97.578
-97.578 442.494
=========== ====================== ===========
========================= Average Values ==========================
Contour Length Sum. Twist
5.358 9.543
=========== ====================== ====================== ===========
The above modulus matrix is in this form:
Where:
\(M_{S}\) - Stretch Modulus
\(M_{T}\) - Twist rigidity
\(M_{S,T}\) - Stretching Twsiting coupling
Convergence in Modulus
Same command can be used to calculate elasticity as a function of time with option -ot/--output-time and save it in csv format file. This result can beused to check their convergence.
If this option is used,
-fgap/--frame-gapis an essential option.This options also gives final value and error as the output on display.
The output file is in csv format and can be opened as spreadsheet.
NOTE: Elastic properties cannot be calculated using a single frame because fluctuations are required. Therefore, here time means trajectory between zero time to given time.
[3]:
%%bash
dnaMD globalElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 20 -estype BST -paxis X -fgap 100 -em block -ot modulus_time_BST.csv
# Print first and last 3 line of output file
echo "====================================="
echo "Elastic modulus as a function of time"
echo "====================================="
head -4 modulus_time_BST.csv
printf ".\n.\n.\n"
tail -3 modulus_time_BST.csv
==============================================
Elasticity Value Error
----------------------------------------------
bend-1 337.233 3.932
bend-2 373.863 4.935
stretch 1080.722 24.015
twist 448.349 29.356
bend-1-bend-2 28.506 4.685
bend-2-stretch 7.977 7.251
stretch-twist -96.198 13.450
bend-1-stretch -6.984 7.131
bend-2-twist 39.509 35.576
bend-1-twist -20.710 5.081
==============================================
=====================================
Elastic modulus as a function of time
=====================================
#Time, bend-1, bend-2, stretch, twist, bend-1-bend-2, bend-2-stretch, stretch-twist, bend-1-stretch, bend-2-twist, bend-1-twist
1000.000, 584.19567, 363.51886, 1121.88830, 1506.57584, 41.49043, -101.57973, 112.06246, -254.22188, -74.92882, 252.68516
2000.000, 354.70978, 367.93829, 1032.49032, 662.58414, -18.43006, -53.55808, 9.82719, -81.25370, -207.81222, 111.70108
3000.000, 380.26015, 359.63694, 967.63012, 543.68667, 5.70038, -76.61296, -8.92719, -88.41420, -95.81366, 56.24528
.
.
.
118000.000, 335.33614, 371.13759, 1082.41850, 449.84105, 27.64596, 10.92246, -97.17016, -7.92023, 36.92839, -17.34603
119000.000, 335.79993, 373.00012, 1081.59948, 449.85747, 28.30290, 9.58966, -96.91853, -6.18165, 37.45497, -19.36140
120000.000, 337.23300, 373.86276, 1080.72201, 448.34909, 28.50566, 7.97658, -96.19760, -6.98413, 39.50860, -20.71008
Some of the plots from above data can be found here
Same as above but only for stretching and twisting motions.
[4]:
%%bash
dnaMD globalElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 20 -estype ST -paxis X -fgap 100 -gt "gmx analyze" -em "block" -ot modulus_time_ST.csv
# Print first and last 3 line of output file
echo "====================================="
echo "Elastic modulus as a function of time"
echo "====================================="
head -4 modulus_time_ST.csv
printf ".\n.\n.\n"
tail -3 modulus_time_ST.csv
==============================================
Elasticity Value Error
----------------------------------------------
stretch 1080.380 22.847
twist 442.494 19.169
stretch-twist -97.578 14.389
==============================================
=====================================
Elastic modulus as a function of time
=====================================
#Time, stretch, twist, stretch-twist
1000.000, 991.91168, 1373.35825, 200.50841
2000.000, 1004.78021, 516.21083, 3.60912
3000.000, 931.30826, 509.38341, -16.08887
.
.
.
118000.000, 1081.86818, 444.95480, -98.78361
119000.000, 1081.20986, 444.61885, -98.34127
120000.000, 1080.37979, 442.49438, -97.57808
Global deformation free energy
To caluclate global deformation enrgy, dnaMD globalEnergy can be used. At first, elastic matrix from reference DNA (most often free or unbound DNA) is calculated and subsequently this matrix is used to calculate deformation free energy of probe DNA (most often bound DNA).
The deformation free energy is calculated using elastic matrix as follows
Where, \(\mathbf{K}\), \(\theta^{x}_0\), \(\theta^{y}_0\), \(L_0\) and \(\phi_0\) is calculated from reference DNA while \(\theta^{x}\), \(\theta^{y}\), \(L\) and \(\phi\) is calculated for probe DNA from each frame.
This command gives output energy as a function of time in csv file and also average energies with error.
[5]:
%%bash
dnaMD globalEnergy -ir free_dna.h5 -ip bound_dna.h5 -tbp 27 -bs 4 -be 20 -estype BST -et "all" -paxis X -gt "gmx analyze" -em "block" -o energy_all_BST.csv
# Print first and last 3 line of output file
echo "==========================================================="
echo "Deformation free energy of bound DNA as a function of time"
echo "==========================================================="
head -4 energy_all_BST.csv
printf ".\n.\n.\n"
tail -3 energy_all_BST.csv
==============================================
Energy(kJ/mol) Average Error
----------------------------------------------
full 27.714 0.724
diag 27.012 0.751
stretch 2.468 0.157
twist 15.061 0.478
st_coupling -0.743 0.040
b1 1.477 0.180
b2 8.005 0.266
bend 9.718 0.386
bs_coupling 0.034 0.002
bt_coupling 0.825 0.020
bb_coupling 0.235 0.020
st 26.269 0.713
bs 11.984 0.499
bt 25.369 0.634
==============================================
===========================================================
Deformation free energy of bound DNA as a function of time
===========================================================
#Time, full, diag, stretch, twist, st_coupling, b1, b2, bend, bs_coupling, bt_coupling, bb_coupling, st, bs, bt
0.000, 29.76525, 29.12752, 3.05586, 16.01787, -0.96687, 0.27243, 9.78136, 10.18484, 0.05805, 1.09664, 0.13105, 28.16064, 13.16770, 27.16829
10.000, 27.69000, 26.82145, 1.78113, 13.65491, -0.68154, 3.00373, 8.38168, 11.78823, 0.02173, 0.69127, 0.40282, 26.13991, 13.18827, 25.73159
20.000, 32.65326, 31.73848, 3.36328, 15.22752, -0.98900, 0.93046, 12.21722, 13.41835, 0.05997, 1.11574, 0.27067, 30.74949, 16.57094, 29.49094
.
.
.
49980.000, 28.48093, 28.59762, 4.40662, 16.38502, -1.17429, 0.45068, 7.35530, 7.95214, 0.05514, 0.91465, 0.14616, 27.42332, 12.26774, 25.10564
49990.000, 33.18350, 32.91519, 3.56658, 21.03477, -1.19700, 0.05849, 8.25534, 8.36962, 0.06281, 1.21256, 0.05579, 31.71819, 11.94323, 30.56117
50000.000, 30.81292, 29.94787, 1.86541, 19.01796, -0.82313, 0.67654, 8.38796, 9.25575, 0.03664, 1.02777, 0.19124, 29.12474, 10.96655, 29.11023
Some of the plots from above data can be found here
Deformation free energy can be calculated as the following terms:
full: Use entire elastic matrix – all motions with their couplingdiag: Use diagonal of elastic matrix – all motions but no couplingb1: Only bending-1 motionb2: Only bending-2 motionstretch: Only stretching motiontwist: Only Twisting motionsst_coupling: Only stretch-twist coupling motionbs_coupling: Only Bending and stretching couplingbt_coupling: Only Bending and Twisting couplingbb_coupling: Only bending-1 and bending-2 couplingbend: Both bending motions with their couplingst: Stretching and twisting motions with their couplingbs: Bending (b1, b2) and stretching motions with their couplingbt: Bending (b1, b2) and twisting motions with their coupling
When all is used, all above terms were calculated.
[6]:
%%bash
dnaMD globalEnergy -ir free_dna.h5 -ip bound_dna.h5 -tbp 27 -bs 4 -be 24 -estype ST -et "all" -gt "gmx analyze" -em "block" -o energy_all_ST.csv
# Print first and last 3 line of output file
echo "==========================================================="
echo "Deformation free energy of bound DNA as a function of time"
echo "==========================================================="
head -4 energy_all_ST.csv
printf ".\n.\n.\n"
tail -3 energy_all_ST.csv
==============================================
Energy(kJ/mol) Average Error
----------------------------------------------
full 15.398 0.353
diag 17.211 0.408
stretch 2.581 0.137
twist 14.630 0.362
st_coupling -0.906 0.037
==============================================
===========================================================
Deformation free energy of bound DNA as a function of time
===========================================================
#Time, full, diag, stretch, twist, st_coupling
0.000, 24.65120, 27.93891, 4.01772, 23.92119, -1.64386
10.000, 16.45031, 18.42131, 2.11880, 16.30251, -0.98550
20.000, 22.50793, 25.46474, 3.54666, 21.91808, -1.47841
.
.
.
49980.000, 13.37563, 15.94228, 5.74292, 10.19936, -1.28332
49990.000, 17.67070, 20.02852, 2.88301, 17.14551, -1.17891
50000.000, 16.73218, 18.89026, 2.53138, 16.35888, -1.07904
Same as above but only for stretching and twisting motions.
Local elastic properties
Local elastic properties can be caluclated using either local base-step parameters or local helical base-step parameters.
In case of base-step parameters: Shift (\(Dx\)), Slide (\(Dy\)), Rise (\(Dz\)), Tilt (\(\tau\)), Roll (\(\rho\)) and Twist (\(\omega\)), following elastic matrix is calculated.
In case of helical-base-step parameters: x-displacement (\(dx\)), y-displacement (\(dy\)), h-rise (\(h\)), inclination (\(\eta\)), tip (\(\theta\)) and twist (\(\Omega\)), following elastic matrix is calculated.
[7]:
%%bash
dnaMD localElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 7 -o local_elasticity_4-7bps.csv
=========== ============== Elastic Matrix =============== ===========
150.32688 -12.74081 -4.99484 -0.86502 -0.08939 -0.16720
-12.74081 129.99578 30.42056 0.27454 -0.58620 -2.06912
-4.99484 30.42056 504.89222 0.65083 -0.06531 0.21751
-0.86502 0.27454 0.65083 0.03433 -0.00104 0.00052
-0.08939 -0.58620 -0.06531 -0.00104 0.01295 0.01427
-0.16720 -2.06912 0.21751 0.00052 0.01427 0.05907
=========== ====================== ====================== ===========
Local elastic properties as a function of time
Same command can be used to calculate elasticity as a function of time with option -ot/--output-time and save it in csv format file. This result can be used to check their convergence.
If this option is used,
-fgap/--frame-gapis an essential option.The output file is in csv format and can be opened as spreadsheet.
NOTE: Elastic properties cannot be calculated using a single frame because fluctuations are required. Therefore, here time means trajectory between zero time to given time.
[8]:
%%bash
dnaMD localElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 7 -fgap 200 -ot local_elasticity_time_4-7bps.csv
# Print first 3 and last 3 line of first seven columns from output file
echo "====================================="
echo "Elastic matrix as a function of time"
echo "====================================="
head -4 local_elasticity_time_4-8bps.csv | awk '{print $1, $2, $3, $4, $5, $6 ,$7, "... ... ..."}'
printf ".\n.\n.\n"
tail -3 local_elasticity_time_4-8bps.csv | awk '{print $1, $2, $3, $4, $5, $6 ,$7, "... ... ..."}'
=====================================
Elastic matrix as a function of time
=====================================
#Time, shift, slide, rise, tilt, roll, twist, ... ... ...
2000.000, 158.96347, 127.71194, 503.26390, 0.03143, 0.01542, 0.05937, ... ... ...
4000.000, 150.93805, 126.16929, 467.98254, 0.03050, 0.01409, 0.06100, ... ... ...
6000.000, 147.43936, 132.39932, 480.47463, 0.03256, 0.01358, 0.06143, ... ... ...
.
.
.
116000.000, 151.11253, 129.64049, 504.93262, 0.03417, 0.01293, 0.05897, ... ... ...
118000.000, 150.77496, 129.62910, 504.85789, 0.03426, 0.01296, 0.05910, ... ... ...
120000.000, 150.32688, 129.99578, 504.89222, 0.03433, 0.01295, 0.05907, ... ... ...
Local elastic properties of the consecutive overlapped DNA segments
Above method gives local elasticities of a small local segment of the DNA. However, we mostly interested in large segment of the DNA. This large segment can be further divided into smaller local segments. For these smaller segments local elasticities can be calculated. Here these segments overlapped with each other.
Same command can be used to calculate elasticity as a function of time with option -os/--output-segments and save it in csv format file.
If this option is used,
-fgap/--frame-gapis an essential option.The output file is in csv format and can be opened as spreadsheet.
[9]:
%%bash
dnaMD localElasticity -i free_dna.h5 -tbp 27 -bs 4 -be 20 -span 4 -fgap 200 -gt "gmx analyze" -em "acf" -os local_elasticity_segments.csv
# Print first 3 and last 3 line of first seven columns from output file
echo "========================================"
echo "Elasticity as a function of DNA segments"
echo "========================================"
head -4 local_elasticity_segments.csv | awk '{print $1, $2, $3, $4, $5, $6 ,$7, "... ... ..."}'
printf ".\n.\n.\n"
tail -3 local_elasticity_segments.csv | awk '{print $1, $2, $3, $4, $5, $6 ,$7, "... ... ..."}'
========================================
Elasticity as a function of DNA segments
========================================
#bps, shift, shift-error, slide, slide-error, rise, rise-error, ... ... ...
4-7, 150.32688, 0.25654, 129.99578, 0.27262, 504.89222, 1.61893, ... ... ...
5-8, 162.67911, 0.46671, 122.65855, 0.47513, 510.18741, 1.36958, ... ... ...
6-9, 172.50587, 2.36981, 119.84961, 1.46698, 510.68380, 2.57983, ... ... ...
.
.
.
15-18, 153.98831, 2.02295, 137.21947, 0.29044, 546.15664, 1.31991, ... ... ...
16-19, 188.51349, 1.91188, 148.97261, 0.46969, 521.74643, 1.14698, ... ... ...
17-20, 174.28796, 2.07481, 134.04039, 0.67123, 573.20011, 2.54414, ... ... ...
Local deformation energy of a local small segment
At first, elastic matrix from reference DNA (most often free or unbound DNA) is calculated and subsequently this matrix is used to calculate deformation free energy of probe DNA (most often bound DNA).
When helical='False'
When helical='True'
[10]:
%%bash
dnaMD localEnergy -ir free_dna.h5 -ip bound_dna.h5 -tbp 27 -bs 10 -be 13 -et all -gt "gmx analyze" -em "block" -o local_energy_time_4-7bps.csv
# Print first 3 and last 3 line from output file
echo "==============================================="
echo "Local deformation energy as a function of time"
echo "==============================================="
head -4 local_energy_time_4-7bps.csv
printf ".\n.\n.\n"
tail -3 local_energy_time_4-7bps.csv
==============================================
Energy(kJ/mol) Average Error
----------------------------------------------
full 19.143 0.671
diag 43.865 1.839
shift 1.366 0.064
slide 15.994 1.069
rise 1.194 0.030
tilt 1.705 0.040
roll 6.365 0.365
twist 17.242 0.781
==============================================
===============================================
Local deformation energy as a function of time
===============================================
#Time, full, diag, shift, slide, rise, tilt, roll, twist
0.000, 32.99568, 97.62372, 0.85609, 43.00855, 0.55182, 0.05174, 8.64099, 44.51453
10.000, 24.91292, 63.21362, 0.18680, 31.85144, 0.31550, 2.74114, 5.80446, 22.31428
20.000, 34.19821, 78.73263, 0.77440, 31.54860, 4.31769, 0.19352, 8.74777, 33.15064
.
.
.
49980.000, 17.43224, 50.92180, 0.07917, 12.95852, 2.46789, 0.92035, 5.74851, 28.74736
49990.000, 18.86625, 58.72850, 3.25713, 25.11722, 0.01483, 1.27080, 1.81182, 27.25671
50000.000, 19.01918, 49.56285, 2.16952, 13.54590, 1.86029, 4.52988, 4.38336, 23.07391
Some of the plots from above data can be found here
Same as the above but energy is calculated using helical base-step parameters
[11]:
%%bash
dnaMD localEnergy -ir free_dna.h5 -ip bound_dna.h5 -tbp 27 -bs 10 -be 13 -et all -helical -gt "gmx analyze" -em "block" -o local_helical_energy_time_4-7bps.csv
# Print first 3 and last 3 line from output file
echo "======================================================"
echo "Local helical deformation energy as a function of time"
echo "======================================================"
head -4 local_energy_time_4-7bps.csv
printf ".\n.\n.\n"
tail -3 local_energy_time_4-7bps.csv
==============================================
Energy(kJ/mol) Average Error
----------------------------------------------
full 18.541 0.607
diag 82.103 3.204
x-disp 38.632 1.974
y-disp 0.940 0.024
h-rise 6.768 0.333
inclination 15.242 0.857
tip 1.288 0.030
h-twist 19.232 0.825
==============================================
======================================================
Local helical deformation energy as a function of time
======================================================
#Time, full, diag, shift, slide, rise, tilt, roll, twist
0.000, 32.99568, 97.62372, 0.85609, 43.00855, 0.55182, 0.05174, 8.64099, 44.51453
10.000, 24.91292, 63.21362, 0.18680, 31.85144, 0.31550, 2.74114, 5.80446, 22.31428
20.000, 34.19821, 78.73263, 0.77440, 31.54860, 4.31769, 0.19352, 8.74777, 33.15064
.
.
.
49980.000, 17.43224, 50.92180, 0.07917, 12.95852, 2.46789, 0.92035, 5.74851, 28.74736
49990.000, 18.86625, 58.72850, 3.25713, 25.11722, 0.01483, 1.27080, 1.81182, 27.25671
50000.000, 19.01918, 49.56285, 2.16952, 13.54590, 1.86029, 4.52988, 4.38336, 23.07391
Deformation energy of the consecutive overlapped DNA segments
Above method gives energy of a small local segment of the DNA. However, we mostly interested in large segment of the DNA. This large segment can be further divided into smaller local segments. For these smaller segments local deformation energy can be calculated. Here these segments overlapped with each other.
[12]:
%%bash
dnaMD localEnergy -ir free_dna.h5 -ip bound_dna.h5 -tbp 27 -bs 4 -be 20 -span 4 -et all -gt "gmx analyze" -em "block" -os local_energy_segments.csv
# Print first 3 and last 3 line from output file
echo "=================================================="
echo "Local deformation energy as a function of segments"
echo "=================================================="
head -4 local_energy_segments.csv
printf ".\n.\n.\n"
tail -3 local_energy_segments.csv
==================================================
Local deformation energy as a function of segments
==================================================
#bps, full, full-error, diag, diag-error, shift, shift-error, slide, slide-error, rise, rise-error, tilt, tilt-error, roll, roll-error, twist, twist-error
4-7, 10.44541, 0.15599, 16.11461, 0.50862, 0.95000, 0.02392, 8.97490, 0.44581, 1.17289, 0.13403, 1.71030, 0.05021, 1.08986, 0.03874, 2.21666, 0.17392
5-8, 9.49626, 0.25053, 19.32846, 0.70809, 1.14060, 0.02737, 9.59726, 0.51038, 1.21808, 0.18759, 1.75363, 0.04521, 1.11454, 0.05955, 4.50435, 0.19880
6-9, 10.52567, 0.28519, 20.09691, 0.54228, 1.22326, 0.02970, 11.45709, 0.43514, 1.51242, 0.08500, 1.90555, 0.04658, 1.31208, 0.11407, 2.68650, 0.09203
.
.
.
15-18, 13.98537, 0.52298, 41.05547, 2.63829, 1.04577, 0.02497, 17.01431, 0.86024, 2.44413, 0.14371, 1.78045, 0.04873, 1.78854, 0.20280, 16.98227, 2.09869
16-19, 14.04847, 0.37844, 39.34525, 1.49491, 1.97148, 0.09511, 14.20378, 0.94662, 2.52573, 0.08194, 1.70940, 0.04099, 0.98835, 0.09072, 17.94652, 1.15043
17-20, 7.89839, 0.32320, 14.91991, 0.78938, 1.03028, 0.02583, 5.81921, 0.49549, 1.40673, 0.06566, 1.46641, 0.03364, 1.05240, 0.14133, 4.14489, 0.38861
Some of the plots from above data can be found here
Same as the above but energy is calculated using helical base-step parameters
[13]:
%%bash
dnaMD localEnergy -ir free_dna.h5 -ip bound_dna.h5 -tbp 27 -bs 4 -be 20 -span 4 -et all -helical -gt "gmx analyze" -em "block" -os local_helical_energy_segments.csv
# Print first 3 and last 3 line from output file
echo "=========================================================="
echo "Local helical deformation energy as a function of segments"
echo "=========================================================="
head -4 local_helical_energy_segments.csv
printf ".\n.\n.\n"
tail -3 local_helical_energy_segments.csv
==========================================================
Local helical deformation energy as a function of segments
==========================================================
#bps, full, full-error, diag, diag-error, x-disp, x-disp-error, y-disp, y-disp-error, h-rise, h-rise-error, inclination, inclination-error, tip, tip-error, h-twist, h-twist-error
4-7, 9.94039, 0.17649, 17.73868, 0.51652, 9.00892, 0.37199, 1.19946, 0.04468, 1.54174, 0.13701, 1.69527, 0.06446, 1.73424, 0.04823, 2.55906, 0.16107
5-8, 9.01980, 0.22539, 19.49642, 0.57573, 8.19696, 0.26473, 1.36335, 0.06127, 1.48339, 0.27526, 1.60444, 0.08879, 1.76889, 0.04544, 5.07939, 0.32815
6-9, 10.30985, 0.26888, 17.00383, 0.38032, 7.38157, 0.25950, 1.96202, 0.28106, 0.99682, 0.02458, 1.68845, 0.14166, 1.89859, 0.04606, 3.07639, 0.16278
.
.
.
15-18, 13.74199, 0.55739, 53.29447, 4.60218, 27.45388, 1.71961, 0.66820, 0.01620, 1.17571, 0.02924, 3.37921, 0.40760, 1.29946, 0.03306, 19.31802, 2.43431
16-19, 12.60741, 0.33640, 46.34514, 2.01539, 19.89670, 0.90439, 0.90573, 0.04403, 1.01976, 0.02504, 1.68335, 0.09711, 1.12857, 0.06776, 21.71103, 1.22043
17-20, 7.54442, 0.33087, 15.27288, 0.76005, 5.60088, 0.40791, 0.91852, 0.02377, 1.13807, 0.02707, 1.66290, 0.20744, 1.25180, 0.02884, 4.70071, 0.43934