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(a)fixed bz2 import, (b)linked to data.peptide in examples/peptide, (c)added a runlog

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tanmoy.7989
2019-09-05 21:19:57 -07:00
parent 96c21bec98
commit 4fdece59a5
5 changed files with 256 additions and 6535 deletions
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7
tools/replica/example/run.sh
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@ -1,10 +1,13 @@
#!/bin/bash
## run REMD using LAMMPS
#mpirun -np 16 ~/mysoftware/lammps/src/lmp_mpi -partition 16x1 -in in.peptide -log log.peptide
mpirun -np 16 ~/mysoftware/lammps/src/lmp_mpi -partition 16x1 -in in.peptide -log log.peptide
## collect all energies from different replica logs
#python parse_ene.py temps.txt log.peptide
echo ; echo
echo "Parsing energies from replica logs"
python parse_ene.py temps.txt log.peptide
## run the reordering tool to get reordered trajectories @ 200 K, 276 K, 400 K
echo ; echo
mpirun -np 16 python ../reorder_remd_traj.py peptide -logfn log.peptide -tfn temps.txt -ns 10 -nw 20 -np 1000 -ot 200 276 400 -logw -e ene.peptide -od ./output