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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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6531
tools/replica/example/data.peptide
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2
tools/replica/example/in.peptide
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@ -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

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

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tools/replica/example/runlog.05Sep19 Normal file
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@ -0,0 +1,249 @@
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...

2
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