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‎level3/solvation-energy/preparation/hbc.gro‎

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@@ -1,63 +1,63 @@
11
ALL ATOM STRUCTURE FOR MOLECULE LIG
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60
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0FJEW H17 1 2.593 1.674 2.000
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0FJEW C41 2 2.497 1.727 2.000
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0FJEW C40 3 2.378 1.655 2.000
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0FJEW H16 4 2.384 1.545 2.000
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0FJEW C11 5 2.254 1.720 2.000
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0FJEW C10 6 2.250 1.862 2.000
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0FJEW C5 7 2.124 1.932 2.000
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0FJEW C4 8 2.003 1.859 2.000
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0FJEW C1 9 1.879 1.927 2.000
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0FJEW C2 10 1.876 2.068 2.000
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0FJEW C3 11 1.997 2.141 2.000
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0FJEW C6 12 2.121 2.073 2.000
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0FJEW C7 13 2.245 2.148 2.000
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0FJEW C8 14 2.369 2.080 2.000
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0FJEW C9 15 2.372 1.935 2.000
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0FJEW C42 16 2.494 1.866 2.000
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0FJEW H18 17 2.590 1.919 2.000
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0FJEW C39 18 2.488 2.155 2.000
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0FJEW H14 19 2.586 2.105 2.000
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0FJEW C38 20 2.485 2.294 2.000
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0FJEW H13 21 2.579 2.351 2.000
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0FJEW C37 22 2.363 2.361 2.000
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0FJEW H15 23 2.365 2.471 2.000
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0FJEW C20 24 2.242 2.290 2.000
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0FJEW C21 25 2.115 2.360 2.000
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0FJEW C22 26 1.994 2.286 2.000
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0FJEW C23 27 1.870 2.355 2.000
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0FJEW C26 28 1.869 2.495 2.000
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0FJEW H3 29 1.775 2.551 2.000
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0FJEW C25 30 1.988 2.567 2.000
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0FJEW H2 31 1.986 2.677 2.000
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0FJEW C24 32 2.110 2.500 2.000
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0FJEW H1 33 2.202 2.560 2.000
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0FJEW C19 34 1.746 2.280 2.000
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0FJEW C17 35 1.750 2.138 2.000
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0FJEW C18 36 1.628 2.065 2.000
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0FJEW C27 37 1.506 2.134 2.000
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0FJEW H6 38 1.410 2.081 2.000
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0FJEW C28 39 1.503 2.273 2.000
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0FJEW H4 40 1.407 2.326 2.000
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0FJEW C29 41 1.622 2.345 2.000
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0FJEW H5 42 1.616 2.455 2.000
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0FJEW C30 43 1.631 1.920 2.000
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0FJEW C15 44 1.755 1.852 2.000
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0FJEW C16 45 1.758 1.710 2.000
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0FJEW C31 46 1.637 1.639 2.000
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0FJEW H7 47 1.635 1.529 2.000
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0FJEW C32 48 1.515 1.706 2.000
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0FJEW H8 49 1.421 1.649 2.000
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0FJEW C33 50 1.512 1.845 2.000
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0FJEW H9 51 1.414 1.895 2.000
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0FJEW C14 52 1.885 1.640 2.000
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0FJEW C13 53 2.006 1.714 2.000
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0FJEW C12 54 2.130 1.645 2.000
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0FJEW C36 55 2.131 1.505 2.000
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0FJEW H10 56 2.225 1.449 2.000
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0FJEW C35 57 2.012 1.433 2.000
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0FJEW H12 58 2.014 1.323 2.000
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0FJEW C34 59 1.890 1.500 2.000
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0FJEW H11 60 1.798 1.440 2.000
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4.00000 4.00000 4.00000
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0FJEW H17 1 2.093 1.174 1.500
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0FJEW C41 2 1.997 1.227 1.500
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0FJEW C40 3 1.878 1.155 1.500
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0FJEW H16 4 1.884 1.045 1.500
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0FJEW C11 5 1.754 1.220 1.500
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0FJEW C10 6 1.750 1.362 1.500
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0FJEW C5 7 1.624 1.432 1.500
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0FJEW C4 8 1.503 1.359 1.500
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0FJEW C1 9 1.379 1.427 1.500
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0FJEW C2 10 1.376 1.568 1.500
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0FJEW C3 11 1.497 1.641 1.500
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0FJEW C6 12 1.621 1.573 1.500
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0FJEW C7 13 1.745 1.648 1.500
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0FJEW C8 14 1.869 1.580 1.500
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0FJEW C9 15 1.872 1.435 1.500
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0FJEW C42 16 1.994 1.366 1.500
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0FJEW H18 17 2.090 1.419 1.500
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0FJEW C39 18 1.988 1.655 1.500
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0FJEW H14 19 2.086 1.605 1.500
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0FJEW C38 20 1.985 1.794 1.500
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0FJEW H13 21 2.079 1.851 1.500
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0FJEW C37 22 1.863 1.861 1.500
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0FJEW H15 23 1.865 1.971 1.500
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0FJEW C20 24 1.742 1.790 1.500
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0FJEW C21 25 1.615 1.860 1.500
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0FJEW C22 26 1.494 1.786 1.500
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0FJEW C23 27 1.370 1.855 1.500
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0FJEW C26 28 1.369 1.995 1.500
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0FJEW H3 29 1.275 2.051 1.500
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0FJEW C25 30 1.488 2.067 1.500
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0FJEW H2 31 1.486 2.177 1.500
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0FJEW C24 32 1.610 2.000 1.500
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0FJEW H1 33 1.702 2.060 1.500
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0FJEW C19 34 1.246 1.780 1.500
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0FJEW C17 35 1.250 1.638 1.500
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0FJEW C18 36 1.128 1.565 1.500
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0FJEW C27 37 1.006 1.634 1.500
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0FJEW H6 38 0.910 1.581 1.500
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0FJEW C28 39 1.003 1.773 1.500
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0FJEW H4 40 0.907 1.826 1.500
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0FJEW C29 41 1.122 1.845 1.500
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0FJEW H5 42 1.116 1.955 1.500
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0FJEW C30 43 1.131 1.420 1.500
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0FJEW C15 44 1.255 1.352 1.500
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0FJEW C16 45 1.258 1.210 1.500
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0FJEW C31 46 1.137 1.139 1.500
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0FJEW H7 47 1.135 1.029 1.500
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0FJEW C32 48 1.015 1.206 1.500
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0FJEW H8 49 0.921 1.149 1.500
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0FJEW C33 50 1.012 1.345 1.500
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0FJEW H9 51 0.914 1.395 1.500
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0FJEW C14 52 1.385 1.140 1.500
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0FJEW C13 53 1.506 1.214 1.500
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0FJEW C12 54 1.630 1.145 1.500
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0FJEW C36 55 1.631 1.005 1.500
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0FJEW H10 56 1.725 0.949 1.500
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0FJEW C35 57 1.512 0.933 1.500
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0FJEW H12 58 1.514 0.823 1.500
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0FJEW C34 59 1.390 1.000 1.500
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0FJEW H11 60 1.298 0.940 1.500
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3.00000 3.00000 3.00000

‎level3/solvation-energy/preparation/inputs/min.mdp‎

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@@ -7,11 +7,11 @@ cutoff-scheme = Verlet
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nstlist = 10
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ns_type = grid
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couple-intramol=yes
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vdw-type = Cut-off
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rvdw = 1.2
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couple-intramol=yes
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coulombtype = pme
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fourierspacing = 0.1
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pme-order = 4

‎level3/solvation-energy/preparation/local-run.sh‎

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gmx=/home/simon/Softwares/gromacs-2024.2/build/bin/gmx
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${gmx} trjconv -f FJEW_allatom_optimised_geometry.pdb -s FJEW_allatom_optimised_geometry.pdb -o hbc.gro -box 3.5 3.5 3.5 -center << EOF
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cp original-topol.top topol.top
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${gmx} trjconv -f FJEW_allatom_optimised_geometry.pdb -s FJEW_allatom_optimised_geometry.pdb -o hbc.gro -box 3 3 3 -center << EOF
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0
1012
0
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EOF
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${gmx} solvate -cs tip4p.gro -cp hbc.gro -o solvated.gro -p topol.top
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${gmx} grompp -f inputs/min.mdp -c solvated.gro -p topol.top -o min -pp min -po min -maxwarn 1
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${gmx} mdrun -v -deffnm min -nt 8
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${gmx} grompp -f inputs/nvt.mdp -c min.gro -p topol.top -o nvt -pp nvt -po nvt -maxwarn 1

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