Commit 4fdece59 authored by tanmoy.7989's avatar tanmoy.7989
Browse files

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

parent 96c21bec

tools/replica/example/data.peptide

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File deleted.

Preview size limit exceeded, changes collapsed.

tools/replica/example/in.peptide

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Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ dihedral_style charmm 
improper_style  harmonic

kspace_style	pppm 0.0001



read_data	    data.peptide

read_data	    ../../../examples/peptide/data.peptide



neighbor	    2.0 bin

neigh_modify	delay 5

tools/replica/example/run.sh

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Original line number Diff line number Diff line 
#!/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

tools/replica/example/runlog.05Sep19

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LAMMPS (7 Aug 2019)

Running on 16 partitions of processors

Setting up tempering ...

Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15

0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

10 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

20 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

30 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

40 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

50 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

60 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

70 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

80 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

90 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

100 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

110 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

120 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

130 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

140 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

150 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

160 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

170 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

180 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

190 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

200 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

210 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

220 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

230 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

240 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

250 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

260 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

270 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

280 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

290 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

300 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

310 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

320 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

330 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

340 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

350 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

360 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

370 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

380 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

390 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

400 5 7 3 9 1 11 0 13 2 15 4 14 6 12 8 10

410 4 6 2 8 0 10 1 12 3 14 5 15 7 13 9 11

420 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

430 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

440 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

450 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

460 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

470 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

480 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

490 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

500 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

510 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

520 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

530 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

540 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

550 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

560 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

570 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

580 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

590 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

600 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

610 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

620 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

630 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

640 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

650 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

660 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

670 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

680 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

690 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

700 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

710 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

720 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

730 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

740 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

750 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

760 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

770 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

780 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

790 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

800 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

810 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

820 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

830 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

840 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

850 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

860 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

870 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

880 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

890 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

900 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

910 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

920 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

930 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

940 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

950 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

960 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

970 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

980 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

990 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1000 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1010 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1020 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1030 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1040 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

1050 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1060 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

1070 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

1080 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

1090 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

1100 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

1110 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1120 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1130 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1140 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1150 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1160 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1170 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1180 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

1190 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1200 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1210 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1220 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1230 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1240 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1250 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1260 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1270 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1280 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1290 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1300 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1310 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1320 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1330 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1340 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1350 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1360 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1370 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1380 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1390 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1400 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1410 7 5 9 3 11 1 13 0 15 2 14 4 12 6 10 8

1420 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1430 7 5 9 3 11 1 13 0 15 2 14 4 12 6 10 8

1440 8 6 10 4 12 2 14 0 15 1 13 3 11 5 9 7

1450 7 5 9 3 11 1 13 0 15 2 14 4 12 6 10 8

1460 8 6 10 4 12 2 14 0 15 1 13 3 11 5 9 7

1470 7 5 9 3 11 1 13 0 15 2 14 4 12 6 10 8

1480 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1490 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1500 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1510 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1520 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1530 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1540 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1550 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1560 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1570 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1580 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1590 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1600 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1610 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1620 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1630 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1640 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1650 7 5 9 3 11 1 13 0 15 2 14 4 12 6 10 8

1660 8 6 10 4 12 2 14 0 15 1 13 3 11 5 9 7

1670 7 5 9 3 11 1 13 0 15 2 14 4 12 6 10 8

1680 6 4 8 2 10 0 12 1 14 3 15 5 13 7 11 9

1690 5 3 7 1 9 0 11 2 13 4 15 6 14 8 12 10

1700 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1710 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1720 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1730 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1740 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1750 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1760 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1770 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1780 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1790 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1800 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1810 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1820 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1830 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1840 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1850 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1860 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1870 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1880 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1890 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1900 4 2 6 0 8 1 10 3 12 5 14 7 15 9 13 11

1910 3 1 5 0 7 2 9 4 11 6 13 8 15 10 14 12

1920 2 0 4 1 6 3 8 5 10 7 12 9 14 11 15 13

1930 1 0 3 2 5 4 7 6 9 8 11 10 13 12 15 14

1940 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

1950 0 2 1 4 3 6 5 8 7 10 9 12 11 14 13 15

1960 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14

1970 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

1980 3 5 1 7 0 9 2 11 4 13 6 15 8 14 10 12

1990 2 4 0 6 1 8 3 10 5 12 7 14 9 15 11 13

2000 1 3 0 5 2 7 4 9 6 11 8 13 10 15 12 14





Parsing energies from replica logs





Getting frames from all replicas at temperature:

200.00 K

209.00 K

219.00 K

230.00 K

241.00 K

252.00 K

264.00 K

276.00 K

289.00 K

303.00 K

317.00 K

332.00 K

348.00 K

365.00 K

382.00 K

400.00 K



Releasing 13 excess procs

Writing buffer to file



Running pymbar...

K (total states) = 16, total samples = 800

N_k = 

[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50]

There are 16 states with samples.

Initializing free energies to zero.

Initial dimensionless free energies with method zeros

f_k = 

[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]

Final dimensionless free energies

f_k = 

[    0.           889.75988663  1792.61111609  2695.06980154

  3515.14636632  4263.62894529  5009.01862104  5689.59180324

  6363.10021193  7023.7847743   7626.11234062  8215.09228661

  8787.37318432  9340.44739436  9844.29510404 10331.10090589]

MBAR initialization complete.



Extracting log-weights...

tools/replica/reorder_remd_traj.py

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@@ -43,7 +43,7 @@ from scipy.special import logsumexp 
from mpi4py import MPI



from tqdm import tqdm, trange

import gzip

import gzip, bz2

try:

    # python-2

    from StringIO import StringIO as IOBuffer

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