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simongravellesimongravelle
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added video PEG
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20 files changed

+14799
-5
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‎level2/stretching-a-polymer/cubic-box/inputs/video.mdp‎

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integrator = md
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dt = 0.002
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nsteps = 300
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nstenergy = 100
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nstlog = 100
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nstxout-compressed = 2
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constraint-algorithm = lincs
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constraints = hbonds
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continuation = no
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coulombtype = pme
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rcoulomb = 1.0
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rlist = 1.0
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vdwtype = Cut-off
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rvdw = 1.0
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tcoupl = v-rescale
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tau_t = 0.1 0.1
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ref_t = 300 300
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tc_grps = PEG Water
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comm-mode = linear
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comm-grps = PEG

‎level2/stretching-a-polymer/cubic-box/local-run.sh‎

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@@ -52,3 +52,8 @@ ${gmx} mk_angndx -s production.tpr -hyd no -type dihedral
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${gmx} angle -n angle.ndx -f production.xtc -od dihedral-distribution.xvg -binwidth 0.25 -type dihedral << EOF
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1
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EOF
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${gmx} grompp -f inputs/video.mdp -c production.gro -p topol.top -o video -maxwarn 1
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${gmx} mdrun -deffnm video -v -nt 8
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${gmx} trjconv -f video.xtc -s video.tpr -o video.xtc -pbc nojump
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‎level2/stretching-a-polymer/cubic-box/mdout.mdp‎

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; File 'mdout.mdp' was generated
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; By user: simon (1000)
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; On host: laptop
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; At date: Fri Jun 7 13:46:34 2024
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; At date: Thu Jun 13 09:00:50 2024
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;
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; Created by:
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; :-) GROMACS - gmx grompp, 2024.2 (-:
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; Data prefix: /home/simon/Softwares/gromacs-2024.2 (source tree)
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; Working dir: /home/simon/Git/GROMACS/inputs/level2/stretching-a-polymer/cubic-box
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; Command line:
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; gmx grompp -f inputs/production-peg-h2o.mdp -c npt.gro -p topol.top -o production -maxwarn 1
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; gmx grompp -f inputs/video.mdp -c production.gro -p topol.top -o video -maxwarn 1
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; VARIOUS PREPROCESSING OPTIONS
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; Preprocessor information: use cpp syntax.
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; Start time and timestep in ps
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tinit = 0
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dt = 0.002
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nsteps = 50000
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nsteps = 500
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; For exact run continuation or redoing part of a run
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init-step = 0
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; Part index is updated automatically on checkpointing (keeps files separate)
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nstcalcenergy = 100
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nstenergy = 100
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; Output frequency and precision for .xtc file
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nstxout-compressed = 100
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nstxout-compressed = 10
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compressed-x-precision = 1000
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; This selects the subset of atoms for the compressed
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; trajectory file. You can select multiple groups. By
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; GENERATE VELOCITIES FOR STARTUP RUN
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gen-vel = no
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gen-temp = 300
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gen-seed = 2097149946
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gen-seed = 2147348391
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; OPTIONS FOR BONDS
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constraints = hbonds

‎level2/stretching-a-polymer/cubic-box/video/em-peg.gro‎

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PEG
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86
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1PEG H 1 2.023 1.637 1.556
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1PEG C 2 1.926 1.632 1.503
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1PEG H1 3 1.900 1.735 1.468
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1PEG H2 4 1.938 1.566 1.414
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1PEG O 5 1.826 1.581 1.590
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1PEG H3 6 1.662 1.673 1.500
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1PEG C1 7 1.698 1.571 1.527
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1PEG H4 8 1.704 1.510 1.435
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1PEG H5 9 1.493 1.531 1.580
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1PEG C2 10 1.594 1.507 1.620
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1PEG H6 11 1.604 1.549 1.722
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1PEG O1 12 1.611 1.365 1.624
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1PEG H7 13 1.409 1.322 1.651
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1PEG C3 14 1.507 1.299 1.697
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1PEG H8 15 1.506 1.335 1.803
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1PEG H9 16 1.426 1.100 1.712
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1PEG C4 17 1.526 1.147 1.696
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1PEG H10 18 1.563 1.117 1.595
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1PEG O2 19 1.615 1.103 1.798
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1PEG H11 20 1.670 0.929 1.894
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1PEG C5 21 1.645 0.963 1.791
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1PEG H12 22 1.557 0.904 1.757
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1PEG H13 23 1.801 0.829 1.723
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1PEG C6 24 1.767 0.933 1.703
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1PEG H14 25 1.848 1.004 1.731
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1PEG O3 26 1.735 0.946 1.565
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1PEG H15 27 1.862 0.816 1.461
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1PEG C7 28 1.847 0.925 1.478
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1PEG H16 29 1.940 0.967 1.523
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1PEG H17 30 1.789 1.100 1.368
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1PEG C8 31 1.826 0.997 1.345
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1PEG H18 32 1.924 1.005 1.293
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1PEG O4 33 1.733 0.929 1.260
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1PEG H19 34 1.665 1.106 1.172
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1PEG C9 35 1.700 1.004 1.144
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1PEG H20 36 1.790 1.013 1.079
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1PEG H21 37 1.607 0.829 1.056
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1PEG C10 38 1.587 0.938 1.064
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1PEG H22 39 1.585 0.982 0.962
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1PEG O5 40 1.461 0.961 1.127
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1PEG H23 41 1.370 0.795 1.039
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1PEG C11 42 1.351 0.904 1.056
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1PEG H24 43 1.338 0.955 0.958
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1PEG H25 44 1.149 0.842 1.105
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1PEG C12 45 1.223 0.918 1.139
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1PEG H26 46 1.249 0.895 1.245
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1PEG O6 47 1.165 1.047 1.124
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1PEG H27 48 1.188 1.115 1.320
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1PEG C13 49 1.108 1.097 1.245
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1PEG H28 50 1.036 1.023 1.286
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1PEG H29 51 0.964 1.217 1.135
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1PEG C14 52 1.033 1.229 1.222
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1PEG H30 53 0.973 1.252 1.313
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1PEG O7 54 1.124 1.336 1.198
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1PEG H31 55 0.979 1.451 1.101
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1PEG C15 56 1.059 1.462 1.178
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1PEG H32 57 1.012 1.496 1.273
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1PEG H33 58 1.102 1.651 1.082
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1PEG C16 59 1.159 1.567 1.129
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1PEG H34 60 1.223 1.520 1.052
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1PEG O8 61 1.237 1.619 1.237
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1PEG H35 62 1.310 1.775 1.116
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1PEG C17 63 1.346 1.699 1.190
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1PEG H36 64 1.421 1.634 1.141
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1PEG H37 65 1.427 1.706 1.391
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1PEG C18 66 1.413 1.775 1.305
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1PEG H38 67 1.512 1.810 1.270
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1PEG O9 68 1.333 1.887 1.345
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1PEG H39 69 1.448 1.915 1.518
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1PEG C19 70 1.401 1.973 1.436
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1PEG H40 71 1.480 2.030 1.382
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1PEG H41 72 1.226 2.102 1.424
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1PEG C20 73 1.303 2.073 1.500
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1PEG H42 74 1.359 2.163 1.531
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1PEG O10 75 1.241 2.015 1.615
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1PEG H43 76 1.047 2.088 1.616
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1PEG C21 77 1.142 2.099 1.673
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1PEG H44 78 1.173 2.205 1.672
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1PEG H45 79 1.023 2.101 1.854
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1PEG C22 80 1.120 2.059 1.820
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1PEG H46 81 1.114 1.948 1.826
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1PEG O11 82 1.225 2.109 1.901
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1PEG H47 83 1.302 2.106 2.094
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1PEG C23 84 1.217 2.063 2.036
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1PEG H48 85 1.122 2.096 2.083
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1PEG H49 86 1.224 1.952 2.040
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3.00000 3.00000 3.00000

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