main
Nova Pratiwi Indriyani 2 years ago
parent be5cb3dce0
commit 8032b6879d
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      README.md
  2. 12
      bin/cmmde.py
  3. 0
      cmmde_gui/gui.py
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      cmmde_gui/ts_finder.py
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      examples/energetics/ch4/IR.pdf
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      examples/energetics/ch4/IR_fit.dat
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      examples/energetics/ch4/cmmd.engrad
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      examples/energetics/ch4/cmmd.gbw
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      examples/energetics/ch4/cmmd.hess
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      examples/energetics/ch4/cmmd.in
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      examples/energetics/ch4/cmmd.opt
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      examples/energetics/ch4/cmmd.out
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      examples/energetics/ch4/cmmd.xtbrestart
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      examples/energetics/ch4/cmmd.xyz
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      examples/energetics/ch4/cmmd_property.txt
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      examples/energetics/ch4/cmmd_trj.xyz
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      examples/energetics/ch4/geom.smi
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      examples/energetics/ch4/geom.xyz
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      examples/energetics/ch4/run.sh
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      examples/energetics/ch4/run_babel.sh
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      examples/energetics/ch4/slurm-2576.out
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      examples/energetics/ch4/slurm-2577.out
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      examples/energetics/ch4/slurm-2602.out
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      examples/energetics/co2/cmmd.engrad
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      examples/energetics/co2/cmmd.gbw
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      examples/energetics/co2/cmmd.hess
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      examples/energetics/co2/cmmd.in
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      examples/energetics/co2/cmmd.opt
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      examples/energetics/co2/cmmd.out
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      examples/energetics/co2/cmmd.xtbrestart
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      examples/energetics/co2/cmmd.xyz
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      examples/energetics/co2/cmmd_property.txt
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      examples/energetics/co2/cmmd_trj.xyz
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      examples/energetics/co2/geom.smi
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      examples/energetics/co2/geom.xyz
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      examples/energetics/co2/run.sh
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      examples/energetics/co2/run_babel.sh
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      examples/energetics/co2/slurm-2578.out
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      examples/energetics/co2/slurm-2579.out
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      examples/energetics/co2/slurm-2603.out
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      examples/energetics/h2o/cmmd.engrad
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      examples/energetics/h2o/cmmd.gbw
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      examples/energetics/h2o/cmmd.hess
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      examples/energetics/h2o/cmmd.in
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      examples/energetics/h2o/cmmd.opt
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      examples/energetics/h2o/cmmd.out
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      examples/energetics/h2o/cmmd.xtbrestart
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      examples/energetics/h2o/cmmd.xyz
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      examples/energetics/h2o/cmmd_property.txt
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      examples/energetics/h2o/cmmd_trj.xyz
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      examples/energetics/h2o/geom.smi
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      examples/energetics/h2o/geom.xyz
  53. 0
      examples/energetics/h2o/run.sh
  54. 0
      examples/energetics/h2o/run_babel.sh
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      examples/energetics/h2o/slurm-2580.out
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      examples/energetics/h2o/slurm-2581.out
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      examples/energetics/h2o/slurm-2604.out
  58. 0
      examples/energetics/o2/cmmd.engrad
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      examples/energetics/o2/cmmd.gbw
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      examples/energetics/o2/cmmd.hess
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      examples/energetics/o2/cmmd.in
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      examples/energetics/o2/cmmd.opt
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      examples/energetics/o2/cmmd.out
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      examples/energetics/o2/cmmd.xtbrestart
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      examples/energetics/o2/cmmd.xyz
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      examples/energetics/o2/cmmd_property.txt
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      examples/energetics/o2/cmmd_trj.xyz
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      examples/energetics/o2/geom.smi
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      examples/energetics/o2/geom.xyz
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      examples/energetics/o2/run.sh
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      examples/energetics/o2/run_babel.sh
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      examples/energetics/o2/slurm-2582.out
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      examples/energetics/o2/slurm-2583.out
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      examples/energetics/o2/slurm-2605.out
  75. 0
      examples/larutan/UreaAir/SistemLarutan/SLV.ndx
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      examples/larutan/UreaAir/SistemLarutan/URA.ndx
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      examples/larutan/UreaAir/SistemLarutan/em.mdp
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      examples/larutan/UreaAir/SistemLarutan/finalsystem.pdb
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      examples/larutan/UreaAir/SistemLarutan/leap.log
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      examples/larutan/UreaAir/SistemLarutan/md.mdp
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      examples/larutan/UreaAir/SistemLarutan/mdout.mdp
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      examples/larutan/UreaAir/SistemLarutan/mini.edr
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      examples/larutan/UreaAir/SistemLarutan/mini.gro
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      examples/larutan/UreaAir/SistemLarutan/mini.log
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      examples/larutan/UreaAir/SistemLarutan/mini.ndx
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      examples/larutan/UreaAir/SistemLarutan/mini.tpr
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      examples/larutan/UreaAir/SistemLarutan/mini.trr
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      examples/larutan/UreaAir/SistemLarutan/minim.mdp
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      examples/larutan/UreaAir/SistemLarutan/msd_SLV.xvg
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      examples/larutan/UreaAir/SistemLarutan/msd_URA.xvg
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      examples/larutan/UreaAir/SistemLarutan/npt.cpt
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      examples/larutan/UreaAir/SistemLarutan/npt.edr
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      examples/larutan/UreaAir/SistemLarutan/npt.gro
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      examples/larutan/UreaAir/SistemLarutan/npt.log
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      examples/larutan/UreaAir/SistemLarutan/npt.mdp
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      examples/larutan/UreaAir/SistemLarutan/npt.tpr
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      examples/larutan/UreaAir/SistemLarutan/npt.trr
  98. 0
      examples/larutan/UreaAir/SistemLarutan/nve.cpt
  99. 0
      examples/larutan/UreaAir/SistemLarutan/nve.edr
  100. 0
      examples/larutan/UreaAir/SistemLarutan/nve.gro
  101. Some files were not shown because too many files have changed in this diff Show More

@ -70,7 +70,7 @@ parser.add_argument('-ctype','--charge_type',type=str, default='gas', help='Tipe
parser.add_argument('-Nump','--NumPelarut', type=int, default=100, help='Jumlah molekul pelarut maksimum dalam sistem larutan. Default = 100.') parser.add_argument('-Nump','--NumPelarut', type=int, default=100, help='Jumlah molekul pelarut maksimum dalam sistem larutan. Default = 100.')
parser.add_argument('-cat','--cation',type=str, default='none',help='Kation yang digunakan untuk menetralkan muatan sistem larutan.') parser.add_argument('-cat','--cation',type=str, default='none',help='Kation yang digunakan untuk menetralkan muatan sistem larutan.')
parser.add_argument('-p', '--pressure', default=1.0, type=float, help='Tekanan dalam satuan bar') parser.add_argument('-p', '--pressure', default=1.0, type=float, help='Tekanan dalam satuan bar')
parser.add_argument('--packmol', type=str, default='/home/adit/opt/packmol/packmol') parser.add_argument('--packmol', type=str, default='packmol')
# Opsi untuk melakukan restart simulasi MD # Opsi untuk melakukan restart simulasi MD
parser.add_argument('-traj','--traject',type=str, default='../NVT/traject',help='File trayektori dari simulasi sebelumnya') parser.add_argument('-traj','--traject',type=str, default='../NVT/traject',help='File trayektori dari simulasi sebelumnya')
parser.add_argument('-vel','--velocity',type=str, default='../NVT/velocity',help='File kecepatan atom dari simulasi sebelumnya') parser.add_argument('-vel','--velocity',type=str, default='../NVT/velocity',help='File kecepatan atom dari simulasi sebelumnya')
@ -464,6 +464,7 @@ mv traject traject.xyz""".format(opt.nproc),file=fout)
os.system('sbatch run.sh') os.system('sbatch run.sh')
if opt.software == 'gromacs': if opt.software == 'gromacs':
if opt.slurm == 'true':
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -474,6 +475,15 @@ export OMP_NUM_THREADS={}
cd $PWD cd $PWD
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress),file=fout) $GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress),file=fout)
os.system('sbatch run.sh') os.system('sbatch run.sh')
else:
with open('run.sh','w') as fout:
print("""#!/bin/bash
export OMP_NUM_THREADS={}
cd $PWD
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress),file=fout)
os.system('chmod +x run.sh')
os.system('./run.sh')
if opt.job == 'proprep' and opt.software == 'gmx': if opt.job == 'proprep' and opt.software == 'gmx':
proprep(opt.protein) proprep(opt.protein)

Some files were not shown because too many files have changed in this diff Show More

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