Updated workflow

README.md

@@ -50,21 +50,23 @@ We will use the program [PARENT](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.5
     - Make sure all trajectories (.xyz files) are inside Processing/ntraj/ first
     - The 6 indices should be 6 13 4 14 10 12
     - Either use interactive input or traj.conf (1st line: reset? y/n 2nd line: bifurcation mode (1 or 2) 3rd line: indices of forming bonds)
-    - For trajectories that have not yet been rearranged such as those generated by Progdyn, uncomment lines 339 and 340 and remove 341
-    - It may be necessary to change the RUNPOINT_IDX on line 18 to ensure that the runpoint is found in the trajectories properly
+    - The function of processing trajectories including obtaining TS sampling ensembles, rearrangement, classification can be implemnted via this script. If trajectories have been rearranged , comment line 306.
+    - It may be necessary to change the RUNPOINT_IDX on line 19 to ensure that the runpoint is found in the trajectories properly
 2. Truncation - run Truncation.py 
+    - Cut off the trajectory starting from the position where bond(4,14) length is 5.00Å and stopping when the bond(4,14) length is 1.58Å for the first time
 3. Slicing - run Subsection.py
-    - Adjust the bond lengths on lines 26-27 to select the subsection in question.
-    - Refer to cycloaddition_TS_irc_rev.log for the intrinsic reaction coordinate (IRC) calculation that bridges cycloaddtion TS1 to Cope TS2, and to cope_TS_irc_rev.log for the IRC that bridges Cope TS2 to the product with formation of bond (4,14).
-
+    - Combination all the trajectories that form product A(i.e., formation of bond(4,14))
+    - The bond(4,14) length range is 2.90Å to 1.58Å, refer to cycloaddition_TS_irc_rev.log for the intrinsic reaction coordinate (IRC) calculation that bridges cycloaddtion TS1 to Cope TS2, and to cope_TS_irc_rev.log for the IRC that bridges Cope TS2 to the product with formation of bond (4,14).
+    - Divide the bond length range into N(ten here) equal parts and adjust the bond lengths on lines 31-32 to select the subsection in question.
+    - Count the number of points falling into the range for convergence analysis
 ### Section 3 - Analysis with PARENT (Code adopted from https://github.com/markusfleck/PARENT)
 1. Convert the subsectioned .xyz files to .xtc
 
         python3 xyz2xtc.py
 
     - Be sure to adjust the file names inside to get all trajectories from the Subsection folder
     - The mdtraj module may need to be installed if not already present
-2. Move all .xtc files and the .top file from Section 1 to test_system inside PARENT-master
+2. Move all .xtc files and the .top file from Section 2 and 1 to test_system inside PARENT-master
 3. Revise the path TRJ and TOP inside PARENT-master/parameters-xin
 4. Run PARENT
     1. Make sure you have the latest versions of GCC and OpenMPI
@@ -76,8 +78,7 @@ We will use the program [PARENT](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.5
     5. Run run.sh with the parameters file
 
             ./run.sh parameter-xin
-
-5. Make a directory inside PARENT-master called total_outputs and move PARENT-master_MIST.txt in every output file into total_outputs
-6. Run entropy_anal.py - total_outputs.xls and D1_D2_conf.txt are the analysis files.(the units of numbers in output files are k<sub>b</sub>)
 
-        python3 entropy_anal.py
+5. Obtain the total configuration entropy from PARENT-master_MIST.txt in each output file.(the units of numbers in output files are k<sub>b</sub>, unit conversion method from k<sub>b</sub> to kcal/mol is in the output analysis file)   
+
+

scripts/ParentAnalysis/2.768_2.636_bondlength/PARENT-master_MIE_topology.txt

@@ -0,0 +1,63 @@
+#bond #atom1 #atom2 
+1 8 5
+2 5 4
+3 4 6
+4 8 9
+5 8 10
+6 6 1
+7 6 7
+8 6 13
+9 10 11
+10 1 2
+11 1 3
+12 13 12
+13 13 16
+14 13 20
+15 12 15
+16 12 18
+17 20 14
+18 20 21
+19 20 22
+20 18 19
+21 14 17
+#angle #atom1 #atom2 #atom3
+1 8 5 4
+2 5 4 6
+3 4 8 9
+4 4 8 10
+5 4 6 1
+6 4 6 7
+7 4 6 13
+8 8 10 11
+9 6 1 2
+10 6 1 3
+11 6 13 12
+12 6 13 16
+13 6 13 20
+14 13 12 15
+15 13 12 18
+16 13 20 14
+17 13 20 21
+18 13 20 22
+19 12 18 19
+20 20 14 17
+#dihedral #atom1 #atom2 #atom3 #atom4    dihedral_type(common=0,pseudo=1,improper=-1)   phaseangle_of(-1 if no phaseangle)
+1 8 5 4 6 -1 -1
+2 5 4 8 9 0 -1
+3 5 4 8 10 0 2
+4 5 4 6 1 0 -1
+5 5 4 6 7 0 4
+6 5 4 6 13 0 4
+7 4 8 10 11 0 -1
+8 4 6 1 2 0 -1
+9 4 6 1 3 0 8
+10 4 6 13 12 0 -1
+11 4 6 13 16 0 10
+12 4 6 13 20 0 10
+13 6 13 12 15 0 14
+14 6 13 12 18 0 -1
+15 6 13 20 14 0 -1
+16 6 13 20 21 0 15
+17 6 13 20 22 0 15
+18 13 12 18 19 0 -1
+19 13 20 14 17 0 -1

scripts/ParentAnalysis/2.768_2.636_bondlength/PARENT-master_MIST.txt

@@ -0,0 +1,69 @@
+b b 1 5   MI: 2.86029051281   left to process: 59
+b b 5 16   MI: 3.38151888536   left to process: 58
+b b 16 7   MI: 3.31864240666   left to process: 57
+b a 5 9   MI: 3.31864240666   left to process: 56
+b a 16 3   MI: 3.30120080187   left to process: 55
+b a 16 10   MI: 3.28375919708   left to process: 54
+b a 16 14   MI: 3.25576592796   left to process: 53
+b a 5 19   MI: 3.25576592796   left to process: 52
+b b 16 10   MI: 3.23832432316   left to process: 51
+b a 16 15   MI: 3.23832432316   left to process: 50
+b b 5 14   MI: 3.23832432316   left to process: 49
+b d 5 9   MI: 3.23832432316   left to process: 48
+b d 16 18   MI: 3.23524200274   left to process: 47
+b a 16 16   MI: 3.22088271837   left to process: 46
+b a 16 6   MI: 3.22088271837   left to process: 45
+b b 5 13   MI: 3.20955611592   left to process: 44
+b b 16 9   MI: 3.19288944925   left to process: 43
+b b 16 19   MI: 3.19288944925   left to process: 42
+b a 16 20   MI: 3.19288944925   left to process: 41
+b d 16 7   MI: 3.17544784446   left to process: 40
+b a 16 12   MI: 3.17544784446   left to process: 39
+b d 16 8   MI: 3.15800623967   left to process: 38
+b d 16 10   MI: 3.15800623967   left to process: 37
+b b 5 11   MI: 3.15800623967   left to process: 36
+b d 5 5   MI: 3.15492391924   left to process: 35
+b d 16 13   MI: 3.13001297055   left to process: 34
+b d 16 1   MI: 3.12923803242   left to process: 33
+b d 16 4   MI: 3.12923803242   left to process: 32
+b d 16 14   MI: 3.12923803242   left to process: 31
+b d 16 19   MI: 3.11257136576   left to process: 30
+b a 16 11   MI: 3.09512976096   left to process: 29
+b a 16 4   MI: 3.09512976096   left to process: 28
+b b 5 17   MI: 3.09512976096   left to process: 27
+a a 14 13   MI: 3.09204744054   left to process: 26
+b b 16 15   MI: 3.06713649184   left to process: 25
+b a 16 8   MI: 3.03759334647   left to process: 24
+b a 16 18   MI: 3.03225328226   left to process: 23
+b b 16 20   MI: 3.02917096183   left to process: 22
+b b 16 6   MI: 3.01481167747   left to process: 21
+b d 16 6   MI: 3.00348507501   left to process: 20
+b a 16 1   MI: 2.98681840835   left to process: 19
+b d 7 15   MI: 2.98604347022   left to process: 18
+b d 5 2   MI: 2.98604347022   left to process: 17
+b d 16 11   MI: 2.96937680356   left to process: 16
+a d 9 12   MI: 2.94060859631   left to process: 15
+a a 8 2   MI: 2.93983365818   left to process: 14
+a a 10 7   MI: 2.93141127354   left to process: 13
+b a 16 17   MI: 2.92316699152   left to process: 12
+b b 16 21   MI: 2.88905872006   left to process: 11
+b d 16 17   MI: 2.84284890802   left to process: 10
+b b 16 12   MI: 2.8420739699   left to process: 9
+b a 16 5   MI: 2.83152230557   left to process: 8
+b b 5 4   MI: 2.79741403411   left to process: 7
+b b 7 18   MI: 2.79129903177   left to process: 6
+b b 16 2   MI: 2.77385742698   left to process: 5
+a d 10 3   MI: 2.76632101249   left to process: 4
+a b 10 3   MI: 2.6791304206   left to process: 3
+b b 16 8   MI: 2.65344453378   left to process: 2
+a d 13 16   MI: 2.59342263438   left to process: 1
+TOTAL 1D BONDS ENTROPY = -35.1908738589
+TOTAL 1D ANGLES ENTROPY = -40.9374626747
+TOTAL 1D DIHEDRALS ENTROPY = -29.1395352944
+TOTAL 2D BONDS-BONDS MUTUAL INFORMATION = 57.743838314
+TOTAL 2D BONDS-ANGLES MUTUAL INFORMATION = 56.1443055918
+TOTAL 2D BONDS-DIHEDRALS MUTUAL INFORMATION = 49.5380467295
+TOTAL 2D ANGLES-ANGLES MUTUAL INFORMATION = 8.96329237226
+TOTAL 2D ANGLES-DIHEDRALS MUTUAL INFORMATION = 8.30035224318
+TOTAL 2D DIHEDRALS-DIHEDRALS MUTUAL INFORMATION = 0
+TOTAL CONFIGURATIONAL ENTROPY = -285.957707079

scripts/ParentAnalysis/2.768_2.636_bondlength/log.txt

@@ -0,0 +1,180 @@
+tc6000
+2021年 09月 02日 星期四 19:57:05 CST
+Working directory is /public/home/QZX_HG/qzx/Dynamics/Software/Parent/test/PARENT-master
+make: 对“all”无需做任何事。
+
+
+
+
+
+    BAT_builder, a program to convert a molecular dynamics trajectory from Cartesian to internal bond-angle-torsion coordinates
+    Copyright (C) 2015  Markus Fleck (member of the laboratory of Bojan Zagrovic, University of Vienna)
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License  version 3
+    as published by the Free Software Foundation.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+    A scientific publication about this program has been released in the Journal of Chemical Theory and Computation:
+    "PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems"
+    DOI: 10.1021/acs.jctc.5b01217
+
+    Please include this citation in works that publish results generated using
+    this program or any modifications of this program.
+
+
+
+
+
+Reading topology.
+Building BAT topology.
+Found 19 dihedrals/impropers.
+Writing .bat trajectory.
+Processed 30 frames.
+Finished writing trajectory.
+--------------------------------------------------------------------------
+The following command line options and corresponding MCA parameter have
+been deprecated and replaced as follows:
+
+  Command line options:
+    Deprecated:  --cpus-per-proc, -cpus-per-proc, --cpus-per-rank, -cpus-per-rank
+    Replacement: --map-by <obj>:PE=N, default <obj>=NUMA
+
+  Equivalent MCA parameter:
+    Deprecated:  rmaps_base_cpus_per_proc
+    Replacement: rmaps_base_mapping_policy=<obj>:PE=N, default <obj>=NUMA
+
+The deprecated forms *will* disappear in a future version of Open MPI.
+Please update to the new syntax.
+--------------------------------------------------------------------------
+[tc6000:34461] SETTING BINDING TO CORE
+[tc6000:34461] MCW rank 0 bound to socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]]: [BB/BB/BB/BB/../../../../../..][../../../../../../../../../..]
+[tc6000:34461] 1 more process has sent help message help-orte-rmaps-base.txt / deprecated
+[tc6000:34461] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
+MPI PROCESS: 0, NODENAME: tc6000, MAXTHREADS: 4, NUMTHREADS: 8
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 3
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 2
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 0
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 1
+
+
+
+
+
+    PARENT, a parallel program to compute the configurational entropy from a molecular dynamics trajectory
+    Copyright (C) 2015  Markus Fleck (member of the laboratory of Bojan Zagrovic, University of Vienna)
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License  version 3
+    as published by the Free Software Foundation.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+    A scientific publication about this program has been released in the Journal of Chemical Theory and Computation:
+    "PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems"
+    DOI: 10.1021/acs.jctc.5b01217
+
+    Please include this citation in works that publish results generated using
+    this program or any modifications of this program.
+
+
+
+
+
+Reading file PARENT-master.bat .
+PARENT-master.bat specs:
+Precision: double #Atoms: 22 #Frames: 30
+Reading frame 0 and the following.
+READIN AND DISTRIBUTION COMPLETED FOR MPI PROCESS 0.
+CALCULATION OF EXTREMA COMPLETED FOR RANK 0.
+1D BONDS CALCULATION COMPLETED FOR MPI PROCESS 0.
+1D ANGLES CALCULATION COMPLETED FOR MPI PROCESS 0.
+1D DIHEDRALS CALCULATION COMPLETED FOR MPI PROCESS 0.
+2D BONDS-BONDS, BONDS-ANGLES AND BONDS-DIHEDRALS CALCULATION COMPLETED FOR MPI PROCESS 0.
+2D ANGLES-ANGLES AND ANGLES-DIHEDRALS CALCULATION COMPLETED FOR MPI PROCESS 0.
+2D DIHEDRALS-DIHEDRALS CALCULATION COMPLETED FOR MPI PROCESS 0.
+MPI PROCESS 0 FINISHED.
+Initialization + readin time: 8.41912
+Calculation time: 0.009405
+Output time: 0.000129
+Total execution time: 8.42866
+PROGRAM FINISHED SUCCESSFULLY.
+--------------------------------------------------------------------------
+The following command line options and corresponding MCA parameter have
+been deprecated and replaced as follows:
+
+  Command line options:
+    Deprecated:  --cpus-per-proc, -cpus-per-proc, --cpus-per-rank, -cpus-per-rank
+    Replacement: --map-by <obj>:PE=N, default <obj>=NUMA
+
+  Equivalent MCA parameter:
+    Deprecated:  rmaps_base_cpus_per_proc
+    Replacement: rmaps_base_mapping_policy=<obj>:PE=N, default <obj>=NUMA
+
+The deprecated forms *will* disappear in a future version of Open MPI.
+Please update to the new syntax.
+--------------------------------------------------------------------------
+[tc6000:00732] SETTING BINDING TO CORE
+[tc6000:00732] MCW rank 0 bound to socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]]: [BB/BB/BB/BB/../../../../../..][../../../../../../../../../..]
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 0
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 1
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 2
+Initiated process = 0 of NCPU=1 processes on machine=tc6000, thread number 3
+
+
+
+
+
+    A program to calculate the MIST approximation of the configurational entropy from the output of the PARENT program
+    Copyright (C) 2015  Markus Fleck, as a representative of the working group of Bojan Zagrovic, University of Vienna
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License  version 3
+    as published by the Free Software Foundation.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+    A scientific publication about this program has been released in the Journal of Chemical Theory and Computation:
+    "PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems"
+    DOI: 10.1021/acs.jctc.5b01217
+
+    Please include this citation in works that publish results generated using
+    this program or any modifications of this program.
+
+
+
+
+
+MPI PROCESS 0 FINISHED.
+Initialization + readin time: 0.067803
+Calculation time: 0.001439
+Total execution time: 0.069242
+PROGRAM FINISHED SUCCESSFULLY.
+[tc6000:00732] 1 more process has sent help message help-orte-rmaps-base.txt / deprecated
+[tc6000:00732] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
+2021年 09月 02日 星期四 19:57:34 CST