jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #791 from akohlmey/charmm-cmap-docs-reference 

Update CMAP related docs and rebuild example input decks
This commit is contained in:
Steve Plimpton 2018-02-02 14:44:58 -07:00 committed by GitHub
parent 5383035828 9fd1e47968
commit 10d80ba9c3
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
16 changed files with 10819 additions and 10752 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
doc/src/Section_tools.txt
View File

@ -111,14 +111,21 @@ back-and-forth between the CHARMM MD code and LAMMPS.
They are intended to make it easy to use CHARMM as a builder and as a
post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
PDB file with associated CHARMM info, including CHARMM force field
data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert
LAMMPS atom dumps into PDB files.
data, into its LAMMPS equivalent. Support for the CMAP correction of
CHARMM22 and later is available as an option. This tool can also add
solvent water molecules and Na+ or Cl- ions to the system.
Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files.
See the README file in the ch2lmp sub-directory for more information.
These tools were created by Pieter in't Veld (pjintve at sandia.gov)
and Paul Crozier (pscrozi at sandia.gov) at Sandia.
CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and
Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and
Tigran Abramyan, (Clemson University) and
Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
chain tool :h4,link(chain)

4
doc/src/fix_cmap.txt
View File

@ -120,6 +120,10 @@ quantity being minimized), you MUST enable the
[Restrictions:]
To function as expected this fix command must be issued {before} a
"read_data"_read_data.html command but {after} a
"read_restart"_read_restart.html command.
This fix can only be used if LAMMPS was built with the MOLECULE
package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.

5
tools/ch2lmp/.gitignore vendored Normal file
View File

@ -0,0 +1,5 @@
*.dump
*.restart
*.restart1
*.restart2
*.cmap

6499
tools/ch2lmp/example-cmap/1gb1.data
View File

File diff suppressed because it is too large Load Diff

9
tools/ch2lmp/example-cmap/1gb1.in
View File

@ -1,5 +1,5 @@
# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:08:55 EDT 2016
# Command: charmm2lammps.pl -water -ions -border=2.0 all36_prot 1gb1
# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:50:21 EST 2018
# Command: charmm2lammps.pl -border=2.0 -cmap=36 -ions -water all36_prot 1gb1
units real
neigh_modify delay 2 every 1
@ -14,7 +14,10 @@ pair_style lj/charmm/coul/long 8 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
read_data 1gb1.data
# Modify following line to point to the desired CMAP file
fix cmap all cmap charmm36.cmap
fix_modify cmap energy yes
read_data 1gb1.data fix cmap crossterm CMAP
special_bonds charmm
thermo 10

306
tools/ch2lmp/example-cmap/1gb1.log
View File

@ -1,8 +1,8 @@
LAMMPS (5 Oct 2016)
package omp 0
WARNING: OpenMP support not enabled during compilation; using 1 thread only. (../fix_omp.cpp:123)
# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:08:55 EDT 2016
# Command: charmm2lammps.pl -water -ions -border=2.0 all36_prot 1gb1
LAMMPS (17 Jan 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:50:21 EST 2018
# Command: charmm2lammps.pl -border=2.0 -cmap=36 -ions -water all36_prot 1gb1
units real
neigh_modify delay 2 every 1
@ -17,9 +17,13 @@ pair_style lj/charmm/coul/long 8 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
read_data 1gb1.data
# Modify following line to point to the desired CMAP file
fix cmap all cmap charmm36.cmap
Reading potential file charmm36.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data 1gb1.data fix cmap crossterm CMAP
orthogonal box = (-20.8413 -14.5892 -13.805) to (23.4963 14.9692 10.827)
2 by 2 by 2 MPI processor grid
2 by 2 by 1 MPI processor grid
reading atoms ...
2833 atoms
scanning bonds ...
@ -49,91 +53,95 @@ thermo_style multi
timestep 1.0
minimize 0.0 0.0 50 200
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.278254
grid = 45 32 30
stencil order = 5
estimated absolute RMS force accuracy = 0.000317429
estimated relative force accuracy = 9.55928e-07
using double precision FFTs
3d grid and FFT values/proc = 15180 5760
Last active /omp style is kspace_style pppm/omp
3d grid and FFT values/proc = 25530 11520
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 7 5 4
Memory usage per processor = 19.7492 Mbytes
binsize = 7, bins = 7 5 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.54 | 24.61 | 24.65 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -3599.1065 KinEng = 0.0000 Temp = 0.0000
PotEng = -3599.1065 E_bond = 169.6834 E_angle = 103.6483
E_dihed = 583.9669 E_impro = 0.0335 E_vdwl = -776.0899
E_coul = 35419.6941 E_long = -39100.0428 Press = 3623.5803
---------------- Step 10 ----- CPU = 0.2563 (sec) ----------------
TotEng = -5168.1778 KinEng = 0.0000 Temp = 0.0000
PotEng = -5168.1778 E_bond = 120.7538 E_angle = 171.5023
E_dihed = 583.0143 E_impro = 6.5958 E_vdwl = -1034.8022
E_coul = 34737.4006 E_long = -39752.6424 Press = -10232.1944
---------------- Step 20 ----- CPU = 0.4597 (sec) ----------------
TotEng = -5784.4945 KinEng = 0.0000 Temp = 0.0000
PotEng = -5784.4945 E_bond = 110.1359 E_angle = 262.6659
E_dihed = 573.8164 E_impro = 8.5071 E_vdwl = -1050.9646
E_coul = 34464.2659 E_long = -40152.9212 Press = -10843.0328
---------------- Step 30 ----- CPU = 0.6813 (sec) ----------------
TotEng = -6342.0862 KinEng = 0.0000 Temp = 0.0000
PotEng = -6342.0862 E_bond = 146.0247 E_angle = 272.7224
E_dihed = 557.6616 E_impro = 7.1074 E_vdwl = -984.4028
E_coul = 34031.1722 E_long = -40372.3718 Press = -13674.9873
---------------- Step 40 ----- CPU = 0.8599 (sec) ----------------
TotEng = -6821.3956 KinEng = 0.0000 Temp = 0.0000
PotEng = -6821.3956 E_bond = 147.4491 E_angle = 271.5247
E_dihed = 548.2429 E_impro = 7.1832 E_vdwl = -873.4714
E_coul = 33514.8072 E_long = -40437.1312 Press = -12024.8390
---------------- Step 50 ----- CPU = 1.0662 (sec) ----------------
TotEng = -7278.3435 KinEng = 0.0000 Temp = 0.0000
PotEng = -7278.3435 E_bond = 181.9934 E_angle = 288.9107
E_dihed = 541.0050 E_impro = 7.1673 E_vdwl = -501.3825
E_coul = 32665.6923 E_long = -40461.7297 Press = -10391.9829
Loop time of 1.06631 on 8 procs for 50 steps with 2833 atoms
TotEng = -3304.5599 KinEng = 0.0000 Temp = 0.0000
PotEng = -3304.5599 E_bond = 169.6834 E_angle = 103.6483
E_dihed = 583.9669 E_impro = 0.0335 E_vdwl = -776.3982
E_coul = 35482.9694 E_long = -38851.5191 Press = 3844.7433
---------------- Step 10 ----- CPU = 0.3473 (sec) ----------------
TotEng = -4930.6259 KinEng = 0.0000 Temp = 0.0000
PotEng = -4930.6259 E_bond = 104.7992 E_angle = 181.4386
E_dihed = 584.0895 E_impro = 7.5537 E_vdwl = -1028.4574
E_coul = 34837.9592 E_long = -39590.5863 Press = -8420.5689
---------------- Step 20 ----- CPU = 0.7554 (sec) ----------------
TotEng = -5457.1158 KinEng = 0.0000 Temp = 0.0000
PotEng = -5457.1158 E_bond = 121.1716 E_angle = 243.0784
E_dihed = 580.3183 E_impro = 8.9483 E_vdwl = -1040.3321
E_coul = 34593.3894 E_long = -39923.3583 Press = -9942.5587
---------------- Step 30 ----- CPU = 1.1694 (sec) ----------------
TotEng = -6057.2086 KinEng = 0.0000 Temp = 0.0000
PotEng = -6057.2086 E_bond = 120.1005 E_angle = 267.0579
E_dihed = 570.6124 E_impro = 9.3921 E_vdwl = -1025.6144
E_coul = 34318.6209 E_long = -40277.2340 Press = -11617.6026
---------------- Step 40 ----- CPU = 1.6505 (sec) ----------------
TotEng = -6520.0628 KinEng = 0.0000 Temp = 0.0000
PotEng = -6520.0628 E_bond = 135.8622 E_angle = 293.3665
E_dihed = 558.0537 E_impro = 8.6211 E_vdwl = -968.6884
E_coul = 33877.9402 E_long = -40381.7851 Press = -12652.4710
---------------- Step 50 ----- CPU = 2.1052 (sec) ----------------
TotEng = -6931.3243 KinEng = 0.0000 Temp = 0.0000
PotEng = -6931.3243 E_bond = 147.5166 E_angle = 290.5234
E_dihed = 550.9597 E_impro = 9.4741 E_vdwl = -794.7620
E_coul = 33347.2827 E_long = -40437.2965 Press = -11322.9412
Loop time of 2.10544 on 4 procs for 50 steps with 2833 atoms
99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-3599.10649881 -7238.80368107 -7278.34352699
Force two-norm initial, final = 1109.81 247.325
Force max component initial, final = 107.492 37.5055
Final line search alpha, max atom move = 0.00133024 0.0498915
Iterations, force evaluations = 50 87
-3304.55988409 -6893.73171135 -6931.32434601
Force two-norm initial, final = 1135.31 300.792
Force max component initial, final = 107.634 93.2558
Final line search alpha, max atom move = 0.00152738 0.142437
Iterations, force evaluations = 50 82
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46313 | 0.53526 | 0.61611 | 6.9 | 50.20
Bond | 0.0070326 | 0.01008 | 0.013407 | 1.8 | 0.95
Kspace | 0.3364 | 0.41785 | 0.49165 | 8.0 | 39.19
Neigh | 0.035014 | 0.035175 | 0.035337 | 0.1 | 3.30
Comm | 0.058533 | 0.05973 | 0.060792 | 0.3 | 5.60
Output | 0.00039005 | 0.00040504 | 0.00049496 | 0.2 | 0.04
Modify | 0.0015707 | 0.0022006 | 0.0025775 | 0.6 | 0.21
Other | | 0.005615 | | | 0.53
Pair | 1.5485 | 1.5674 | 1.5856 | 1.4 | 74.44
Bond | 0.017887 | 0.020853 | 0.024278 | 1.6 | 0.99
Kspace | 0.41442 | 0.43099 | 0.45053 | 2.5 | 20.47
Neigh | 0.052102 | 0.052125 | 0.052147 | 0.0 | 2.48
Comm | 0.023884 | 0.024002 | 0.024059 | 0.0 | 1.14
Output | 0.00030303 | 0.00051945 | 0.0011663 | 0.0 | 0.02
Modify | 0.0015671 | 0.0018674 | 0.0021205 | 0.5 | 0.09
Other | | 0.007689 | | | 0.37
Nlocal: 354.125 ave 376 max 344 min
Histogram: 3 1 0 1 2 0 0 0 0 1
Nghost: 7405 ave 7531 max 7307 min
Histogram: 1 2 1 0 0 1 1 1 0 1
Neighs: 178281 ave 194848 max 158123 min
Histogram: 2 0 1 0 0 1 0 1 2 1
Nlocal: 708.25 ave 728 max 693 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 9301.25 ave 9410 max 9200 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 356382 ave 367163 max 347323 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1426250
Ave neighs/atom = 503.442
Total # of neighbors = 1425526
Ave neighs/atom = 503.186
Ave special neighs/atom = 4.67702
Neighbor list builds = 4
Neighbor list builds = 3
Dangerous builds = 0
reset_timestep 0
@ -152,105 +160,97 @@ dump_modify 1 image yes scale yes
thermo 100
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.278254
grid = 45 32 30
stencil order = 5
estimated absolute RMS force accuracy = 0.000317429
estimated relative force accuracy = 9.55928e-07
using double precision FFTs
3d grid and FFT values/proc = 15180 5760
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 7 5 4
Memory usage per processor = 20.5221 Mbytes
3d grid and FFT values/proc = 25530 11520
Per MPI rank memory allocation (min/avg/max) = 25.34 | 25.4 | 25.44 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -7547.0017 KinEng = 0.0000 Temp = 0.0000
PotEng = -7547.0017 E_bond = 52.4535 E_angle = 149.7924
E_dihed = 541.0050 E_impro = 7.1673 E_vdwl = -501.3825
E_coul = 32665.6923 E_long = -40461.7297 Press = -9600.9476
---------------- Step 100 ----- CPU = 0.8242 (sec) ----------------
TotEng = -7049.9503 KinEng = 688.1123 Temp = 113.4757
PotEng = -7738.0625 E_bond = 53.8035 E_angle = 139.7846
E_dihed = 529.5460 E_impro = 6.1806 E_vdwl = 52.8666
E_coul = 31951.7370 E_long = -40471.9810 Press = -5991.4443
---------------- Step 200 ----- CPU = 1.6765 (sec) ----------------
TotEng = -7050.0350 KinEng = 956.0848 Temp = 157.6667
PotEng = -8006.1198 E_bond = 47.1331 E_angle = 140.9769
E_dihed = 517.5474 E_impro = 5.7244 E_vdwl = 635.2166
E_coul = 31127.8100 E_long = -40480.5282 Press = -920.9624
---------------- Step 300 ----- CPU = 2.5246 (sec) ----------------
TotEng = -7050.0984 KinEng = 1049.7346 Temp = 173.1104
PotEng = -8099.8330 E_bond = 47.4551 E_angle = 156.5090
E_dihed = 520.6006 E_impro = 9.4008 E_vdwl = 451.0904
E_coul = 31202.3817 E_long = -40487.2707 Press = -2352.9550
---------------- Step 400 ----- CPU = 3.3982 (sec) ----------------
TotEng = -7050.1671 KinEng = 1099.2465 Temp = 181.2753
PotEng = -8149.4136 E_bond = 56.6375 E_angle = 164.5897
E_dihed = 528.8356 E_impro = 8.8390 E_vdwl = 525.0114
E_coul = 31060.0380 E_long = -40493.3650 Press = -2146.9087
---------------- Step 500 ----- CPU = 4.2800 (sec) ----------------
TotEng = -7050.2027 KinEng = 1134.4924 Temp = 187.0877
PotEng = -8184.6951 E_bond = 53.5903 E_angle = 169.1090
E_dihed = 522.9488 E_impro = 7.9830 E_vdwl = 496.8404
E_coul = 31058.9967 E_long = -40494.1633 Press = -2537.1829
---------------- Step 600 ----- CPU = 5.1548 (sec) ----------------
TotEng = -7050.1894 KinEng = 1122.6756 Temp = 185.1390
PotEng = -8172.8649 E_bond = 47.9283 E_angle = 168.7967
E_dihed = 518.7200 E_impro = 9.2011 E_vdwl = 499.6778
E_coul = 31076.1916 E_long = -40493.3805 Press = -1939.2216
---------------- Step 700 ----- CPU = 6.0377 (sec) ----------------
TotEng = -7050.2850 KinEng = 1154.4452 Temp = 190.3781
PotEng = -8204.7301 E_bond = 54.3594 E_angle = 183.8772
E_dihed = 513.0797 E_impro = 9.6842 E_vdwl = 522.0052
E_coul = 31008.3632 E_long = -40496.0990 Press = -2059.4885
---------------- Step 800 ----- CPU = 6.9161 (sec) ----------------
TotEng = -7050.2852 KinEng = 1146.2741 Temp = 189.0306
PotEng = -8196.5593 E_bond = 48.8126 E_angle = 171.3411
E_dihed = 525.8682 E_impro = 10.5588 E_vdwl = 538.6905
E_coul = 31003.8447 E_long = -40495.6752 Press = -1458.5181
---------------- Step 900 ----- CPU = 7.8101 (sec) ----------------
TotEng = -7050.3025 KinEng = 1154.2134 Temp = 190.3398
PotEng = -8204.5159 E_bond = 51.1010 E_angle = 177.9642
E_dihed = 520.6908 E_impro = 8.9539 E_vdwl = 521.5994
E_coul = 31012.6307 E_long = -40497.4560 Press = -1683.9131
---------------- Step 1000 ----- CPU = 8.7313 (sec) ----------------
TotEng = -7050.3166 KinEng = 1179.9351 Temp = 194.5816
PotEng = -8230.2517 E_bond = 57.8905 E_angle = 190.1556
E_dihed = 518.1288 E_impro = 10.0403 E_vdwl = 557.6413
E_coul = 30933.6472 E_long = -40497.7554 Press = -1643.1247
Loop time of 8.73139 on 8 procs for 1000 steps with 2833 atoms
TotEng = -7157.1195 KinEng = 0.0000 Temp = 0.0000
PotEng = -7157.1195 E_bond = 59.0052 E_angle = 144.8137
E_dihed = 550.9597 E_impro = 9.4741 E_vdwl = -794.7620
E_coul = 33347.2827 E_long = -40437.2965 Press = -11653.0907
---------------- Step 100 ----- CPU = 2.0713 (sec) ----------------
TotEng = -6731.9859 KinEng = 736.6132 Temp = 121.4739
PotEng = -7468.5991 E_bond = 51.6809 E_angle = 141.9715
E_dihed = 539.0053 E_impro = 6.5800 E_vdwl = -138.7778
E_coul = 32438.3099 E_long = -40470.2744 Press = -6545.1453
---------------- Step 200 ----- CPU = 4.1194 (sec) ----------------
TotEng = -6732.1577 KinEng = 1137.9916 Temp = 187.6647
PotEng = -7870.1494 E_bond = 54.1322 E_angle = 155.0534
E_dihed = 530.3471 E_impro = 6.0821 E_vdwl = 581.9109
E_coul = 31309.7031 E_long = -40477.5339 Press = -1108.1567
---------------- Step 300 ----- CPU = 6.2051 (sec) ----------------
TotEng = -6732.2356 KinEng = 1205.1394 Temp = 198.7380
PotEng = -7937.3749 E_bond = 50.7295 E_angle = 154.0262
E_dihed = 541.0277 E_impro = 9.6153 E_vdwl = 553.9794
E_coul = 31264.5100 E_long = -40483.0651 Press = -1179.2736
---------------- Step 400 ----- CPU = 8.3309 (sec) ----------------
TotEng = -6732.3498 KinEng = 1263.7920 Temp = 208.4103
PotEng = -7996.1418 E_bond = 59.5441 E_angle = 159.8690
E_dihed = 531.3170 E_impro = 9.8105 E_vdwl = 572.2021
E_coul = 31187.5411 E_long = -40486.5450 Press = -1312.0304
---------------- Step 500 ----- CPU = 10.5236 (sec) ----------------
TotEng = -6732.2697 KinEng = 1225.7309 Temp = 202.1337
PotEng = -7958.0006 E_bond = 52.7184 E_angle = 169.2353
E_dihed = 529.7384 E_impro = 10.4859 E_vdwl = 489.7017
E_coul = 31300.5731 E_long = -40480.8862 Press = -1431.7699
---------------- Step 600 ----- CPU = 12.7351 (sec) ----------------
TotEng = -6732.2989 KinEng = 1238.7683 Temp = 204.2837
PotEng = -7971.0672 E_bond = 56.2994 E_angle = 173.1005
E_dihed = 530.0426 E_impro = 10.5372 E_vdwl = 535.7865
E_coul = 31234.7342 E_long = -40486.0690 Press = -1402.7109
---------------- Step 700 ----- CPU = 14.9715 (sec) ----------------
TotEng = -6732.3516 KinEng = 1309.3540 Temp = 215.9239
PotEng = -8041.7056 E_bond = 59.3741 E_angle = 177.8374
E_dihed = 526.2153 E_impro = 12.2105 E_vdwl = 536.7845
E_coul = 31152.4306 E_long = -40484.9510 Press = -1448.7774
---------------- Step 800 ----- CPU = 17.2110 (sec) ----------------
TotEng = -6732.3114 KinEng = 1299.2723 Temp = 214.2613
PotEng = -8031.5837 E_bond = 55.8605 E_angle = 178.5243
E_dihed = 534.2468 E_impro = 11.5427 E_vdwl = 560.2428
E_coul = 31143.0967 E_long = -40486.6330 Press = -737.0231
---------------- Step 900 ----- CPU = 19.4334 (sec) ----------------
TotEng = -6732.4712 KinEng = 1299.4505 Temp = 214.2907
PotEng = -8031.9217 E_bond = 61.2314 E_angle = 181.8029
E_dihed = 536.4906 E_impro = 12.4741 E_vdwl = 475.8515
E_coul = 31223.2733 E_long = -40494.0221 Press = -1853.8183
---------------- Step 1000 ----- CPU = 21.6519 (sec) ----------------
TotEng = -6732.4953 KinEng = 1325.4723 Temp = 218.5819
PotEng = -8057.9676 E_bond = 55.0903 E_angle = 187.1899
E_dihed = 524.1709 E_impro = 13.3778 E_vdwl = 510.4710
E_coul = 31176.6501 E_long = -40497.1637 Press = -1649.1418
Loop time of 21.6521 on 4 procs for 1000 steps with 2833 atoms
Performance: 9.895 ns/day, 2.425 hours/ns, 114.529 timesteps/s
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
Performance: 3.990 ns/day, 6.014 hours/ns, 46.185 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2841 | 3.856 | 4.393 | 17.3 | 44.16
Bond | 0.041216 | 0.074389 | 0.11041 | 7.2 | 0.85
Kspace | 2.8668 | 3.4354 | 4.0036 | 18.9 | 39.35
Neigh | 0.3024 | 0.30315 | 0.30402 | 0.1 | 3.47
Comm | 0.58794 | 0.60511 | 0.61362 | 1.0 | 6.93
Output | 0.010607 | 0.010696 | 0.010783 | 0.0 | 0.12
Modify | 0.40802 | 0.41482 | 0.42598 | 0.8 | 4.75
Other | | 0.03184 | | | 0.36
Pair | 13.758 | 14.312 | 14.767 | 11.1 | 66.10
Bond | 0.14719 | 0.17763 | 0.21239 | 5.5 | 0.82
Kspace | 5.0774 | 5.5813 | 6.2275 | 18.7 | 25.78
Neigh | 0.81074 | 0.8116 | 0.81234 | 0.1 | 3.75
Comm | 0.28366 | 0.34314 | 0.41466 | 10.2 | 1.58
Output | 0.018707 | 0.019262 | 0.020673 | 0.6 | 0.09
Modify | 0.33949 | 0.35308 | 0.36488 | 1.7 | 1.63
Other | | 0.05392 | | | 0.25
Nlocal: 354.125 ave 390 max 323 min
Histogram: 2 0 2 0 1 0 0 0 1 2
Nghost: 7219.12 ave 7453 max 6941 min
Histogram: 1 1 1 1 0 0 0 0 2 2
Neighs: 179095 ave 217661 max 144647 min
Histogram: 1 0 1 1 1 2 1 0 0 1
Nlocal: 708.25 ave 747 max 669 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 9164.5 ave 9383 max 8916 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 357504 ave 379770 max 327897 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 1432758
Ave neighs/atom = 505.739
Total # of neighbors = 1430018
Ave neighs/atom = 504.772
Ave special neighs/atom = 4.67702
Neighbor list builds = 39
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:09
Total wall time: 0:00:23

3226
tools/ch2lmp/example-cmap/1gb1_ctrl.pdb
View File

File diff suppressed because it is too large Load Diff

3962
tools/ch2lmp/example-cmap/1gb1_ctrl.psf
View File

File diff suppressed because it is too large Load Diff

4
tools/ch2lmp/example-cmap/convert.sh Executable file
View File

@ -0,0 +1,4 @@
#!/bin/sh
rm -f *.dump *.restart? *.restart
../charmm2lammps.pl -border=2.0 -cmap=36 -ions -water all36_prot 1gb1
cp ../../../potentials/charmm36.cmap .

3514
tools/ch2lmp/example/1ac7.data
View File

File diff suppressed because it is too large Load Diff

2
tools/ch2lmp/example/1ac7.in
View File

@ -1,4 +1,4 @@
# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:18:20 EDT 2016
# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:46:18 EST 2018
# Command: charmm2lammps.pl -water -ions -border=2.0 all27_na 1ac7
units real

294
tools/ch2lmp/example/1ac7.log
View File

@ -1,7 +1,7 @@
LAMMPS (5 Oct 2016)
package omp 0
WARNING: OpenMP support not enabled during compilation; using 1 thread only. (../fix_omp.cpp:123)
# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:18:20 EDT 2016
LAMMPS (17 Jan 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:46:18 EST 2018
# Command: charmm2lammps.pl -water -ions -border=2.0 all27_na 1ac7
units real
@ -19,7 +19,7 @@ kspace_style pppm 1e-6
read_data 1ac7.data
orthogonal box = (-14.087 -1.88253 -5.44214) to (10.545 22.7495 33.9691)
2 by 2 by 2 MPI processor grid
2 by 1 by 2 MPI processor grid
reading atoms ...
1968 atoms
scanning bonds ...
@ -49,89 +49,93 @@ thermo_style multi
timestep 1.0
minimize 0.0 0.0 50 200
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.280406
grid = 30 30 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000302577
estimated relative force accuracy = 9.11202e-07
using double precision FFTs
3d grid and FFT values/proc = 13068 4500
Last active /omp style is kspace_style pppm/omp
3d grid and FFT values/proc = 21978 9000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 4 4 6
Memory usage per processor = 15.8614 Mbytes
binsize = 7, bins = 4 4 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.89 | 17.89 | 17.9 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 16313.1962 KinEng = 0.0000 Temp = 0.0000
PotEng = 16313.1962 E_bond = 12014.3479 E_angle = 5414.5475
E_dihed = 557.2338 E_impro = 0.0516 E_vdwl = 1176.0283
E_coul = 28218.0485 E_long = -31067.0615 Press = -18022.1296
---------------- Step 10 ----- CPU = 0.1081 (sec) ----------------
TotEng = -1447.9072 KinEng = 0.0000 Temp = 0.0000
PotEng = -1447.9072 E_bond = 247.8926 E_angle = 2176.8245
E_dihed = 555.8870 E_impro = 1.7628 E_vdwl = -407.3892
E_coul = 27746.6549 E_long = -31769.5399 Press = -1411.7232
---------------- Step 20 ----- CPU = 0.2182 (sec) ----------------
TotEng = -4807.5054 KinEng = 0.0000 Temp = 0.0000
PotEng = -4807.5054 E_bond = 177.3593 E_angle = 555.9353
E_dihed = 551.4306 E_impro = 2.6640 E_vdwl = -581.3001
E_coul = 27120.3184 E_long = -32633.9130 Press = -13576.9371
---------------- Step 30 ----- CPU = 0.3443 (sec) ----------------
TotEng = -5555.1803 KinEng = 0.0000 Temp = 0.0000
PotEng = -5555.1803 E_bond = 147.6057 E_angle = 459.3239
E_dihed = 539.1126 E_impro = 2.8843 E_vdwl = -576.4747
E_coul = 26797.8386 E_long = -32925.4706 Press = -12870.0319
---------------- Step 40 ----- CPU = 0.4657 (sec) ----------------
TotEng = -5973.0779 KinEng = 0.0000 Temp = 0.0000
PotEng = -5973.0779 E_bond = 150.6611 E_angle = 441.4999
E_dihed = 528.1431 E_impro = 3.1819 E_vdwl = -519.1875
E_coul = 26477.1520 E_long = -33054.5284 Press = -13277.6629
---------------- Step 50 ----- CPU = 0.5988 (sec) ----------------
TotEng = -6363.9506 KinEng = 0.0000 Temp = 0.0000
PotEng = -6363.9506 E_bond = 165.0850 E_angle = 401.3082
E_dihed = 518.3931 E_impro = 3.2379 E_vdwl = -463.1261
E_coul = 26138.9684 E_long = -33127.8170 Press = -13085.4188
Loop time of 0.598905 on 8 procs for 50 steps with 1968 atoms
TotEng = 16382.0106 KinEng = 0.0000 Temp = 0.0000
PotEng = 16382.0106 E_bond = 12014.3479 E_angle = 5414.5475
E_dihed = 557.2338 E_impro = 0.0516 E_vdwl = 1174.9839
E_coul = 28273.7003 E_long = -31052.8544 Press = -17947.7297
---------------- Step 10 ----- CPU = 0.2030 (sec) ----------------
TotEng = -1386.3677 KinEng = 0.0000 Temp = 0.0000
PotEng = -1386.3677 E_bond = 238.0964 E_angle = 2167.9109
E_dihed = 556.7458 E_impro = 2.3622 E_vdwl = -407.1366
E_coul = 27803.2765 E_long = -31747.6229 Press = -902.5957
---------------- Step 20 ----- CPU = 0.4523 (sec) ----------------
TotEng = -4643.9749 KinEng = 0.0000 Temp = 0.0000
PotEng = -4643.9749 E_bond = 186.6424 E_angle = 546.1482
E_dihed = 557.6115 E_impro = 3.7530 E_vdwl = -572.4168
E_coul = 27184.6593 E_long = -32550.3724 Press = -13499.9676
---------------- Step 30 ----- CPU = 0.7954 (sec) ----------------
TotEng = -5356.2261 KinEng = 0.0000 Temp = 0.0000
PotEng = -5356.2261 E_bond = 150.5494 E_angle = 451.1209
E_dihed = 548.4804 E_impro = 3.8629 E_vdwl = -587.7229
E_coul = 26908.1173 E_long = -32830.6340 Press = -12635.5249
---------------- Step 40 ----- CPU = 1.1432 (sec) ----------------
TotEng = -5814.9675 KinEng = 0.0000 Temp = 0.0000
PotEng = -5814.9675 E_bond = 145.1741 E_angle = 424.9449
E_dihed = 539.7599 E_impro = 3.8304 E_vdwl = -559.2034
E_coul = 26618.2861 E_long = -32987.7596 Press = -13254.1066
---------------- Step 50 ----- CPU = 1.4855 (sec) ----------------
TotEng = -6207.1556 KinEng = 0.0000 Temp = 0.0000
PotEng = -6207.1556 E_bond = 172.5209 E_angle = 400.9621
E_dihed = 532.0702 E_impro = 3.4517 E_vdwl = -491.3979
E_coul = 26261.2546 E_long = -33086.0173 Press = -13942.2342
Loop time of 1.48576 on 4 procs for 50 steps with 1968 atoms
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
16313.1961904 -6328.33883947 -6363.95060584
Force two-norm initial, final = 9108.55 292.099
Force max component initial, final = 2254.31 67.3492
Final line search alpha, max atom move = 0.00149026 0.100368
16382.0106166 -6167.68761847 -6207.15563509
Force two-norm initial, final = 9111.03 289.249
Force max component initial, final = 2253.01 63.7887
Final line search alpha, max atom move = 0.000835537 0.0532979
Iterations, force evaluations = 50 75
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24051 | 0.28255 | 0.35023 | 7.1 | 47.18
Bond | 0.0022576 | 0.0057876 | 0.0081606 | 2.6 | 0.97
Kspace | 0.18978 | 0.25595 | 0.29717 | 7.2 | 42.74
Neigh | 0.015369 | 0.01561 | 0.015768 | 0.1 | 2.61
Comm | 0.031344 | 0.032818 | 0.034241 | 0.5 | 5.48
Output | 0.00034261 | 0.00035512 | 0.00043511 | 0.2 | 0.06
Modify | 0.0011175 | 0.001414 | 0.0016975 | 0.5 | 0.24
Other | | 0.00442 | | | 0.74
Pair | 0.86139 | 0.95604 | 1.1156 | 10.8 | 64.35
Bond | 0.0054429 | 0.012373 | 0.015879 | 3.7 | 0.83
Kspace | 0.29818 | 0.45076 | 0.54304 | 15.1 | 30.34
Neigh | 0.037995 | 0.038014 | 0.038038 | 0.0 | 2.56
Comm | 0.021986 | 0.022179 | 0.022257 | 0.1 | 1.49
Output | 0.00028157 | 0.00048172 | 0.0010796 | 0.0 | 0.03
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005911 | | | 0.40
Nlocal: 246 ave 274 max 226 min
Histogram: 2 1 0 1 1 0 1 1 0 1
Nghost: 6331 ave 6591 max 6075 min
Histogram: 1 1 0 0 2 2 0 0 1 1
Neighs: 116074 ave 137552 max 99519 min
Histogram: 1 2 1 1 0 0 0 1 0 2
Nlocal: 492 ave 538 max 472 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 8001.25 ave 8242 max 7756 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 232207 ave 275971 max 203927 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 928592
Ave neighs/atom = 471.846
Total # of neighbors = 928828
Ave neighs/atom = 471.965
Ave special neighs/atom = 4.4065
Neighbor list builds = 3
Dangerous builds = 0
@ -152,105 +156,97 @@ dump_modify 1 image yes scale yes
thermo 100
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.280406
grid = 30 30 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000302577
estimated relative force accuracy = 9.11202e-07
using double precision FFTs
3d grid and FFT values/proc = 13068 4500
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 4 4 6
Memory usage per processor = 16.6281 Mbytes
3d grid and FFT values/proc = 21978 9000
Per MPI rank memory allocation (min/avg/max) = 18.67 | 18.68 | 18.68 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -6507.5910 KinEng = 0.0000 Temp = 0.0000
PotEng = -6507.5910 E_bond = 107.6907 E_angle = 315.0621
E_dihed = 518.3931 E_impro = 3.2379 E_vdwl = -463.1261
E_coul = 26138.9684 E_long = -33127.8170 Press = -12385.0996
---------------- Step 100 ----- CPU = 0.6002 (sec) ----------------
TotEng = -6239.1679 KinEng = 693.7285 Temp = 162.5977
PotEng = -6932.8964 E_bond = 97.8328 E_angle = 278.8843
E_dihed = 517.0395 E_impro = 2.5171 E_vdwl = 25.4169
E_coul = 25297.7912 E_long = -33152.3783 Press = -7082.4023
---------------- Step 200 ----- CPU = 1.2143 (sec) ----------------
TotEng = -6239.2467 KinEng = 973.1878 Temp = 228.0980
PotEng = -7212.4345 E_bond = 100.5993 E_angle = 320.4657
E_dihed = 524.2274 E_impro = 2.4292 E_vdwl = 599.6228
E_coul = 24399.1819 E_long = -33158.9608 Press = -876.3929
---------------- Step 300 ----- CPU = 1.8629 (sec) ----------------
TotEng = -6239.3074 KinEng = 1080.8940 Temp = 253.3425
PotEng = -7320.2014 E_bond = 109.8163 E_angle = 341.6580
E_dihed = 522.9161 E_impro = 3.3533 E_vdwl = 548.9557
E_coul = 24315.8677 E_long = -33162.7685 Press = -2189.9473
---------------- Step 400 ----- CPU = 2.5209 (sec) ----------------
TotEng = -6239.4210 KinEng = 1085.2885 Temp = 254.3725
PotEng = -7324.7096 E_bond = 95.4880 E_angle = 333.0840
E_dihed = 531.5762 E_impro = 4.2236 E_vdwl = 547.4841
E_coul = 24332.2081 E_long = -33168.7736 Press = -1741.7706
---------------- Step 500 ----- CPU = 3.1762 (sec) ----------------
TotEng = -6239.4511 KinEng = 1151.8207 Temp = 269.9665
PotEng = -7391.2719 E_bond = 108.9390 E_angle = 328.6496
E_dihed = 528.8096 E_impro = 3.4706 E_vdwl = 499.9982
E_coul = 24309.7254 E_long = -33170.8642 Press = -2725.2316
---------------- Step 600 ----- CPU = 3.8115 (sec) ----------------
TotEng = -6239.4095 KinEng = 1129.5086 Temp = 264.7369
PotEng = -7368.9182 E_bond = 102.3632 E_angle = 346.1347
E_dihed = 534.3048 E_impro = 3.7134 E_vdwl = 473.9210
E_coul = 24346.7523 E_long = -33176.1075 Press = -2684.1848
---------------- Step 700 ----- CPU = 4.4501 (sec) ----------------
TotEng = -6239.4955 KinEng = 1132.8803 Temp = 265.5272
PotEng = -7372.3758 E_bond = 103.5625 E_angle = 340.8027
E_dihed = 535.9840 E_impro = 4.0448 E_vdwl = 488.9549
E_coul = 24323.6826 E_long = -33169.4072 Press = -2041.9019
---------------- Step 800 ----- CPU = 5.0783 (sec) ----------------
TotEng = -6239.5236 KinEng = 1192.2677 Temp = 279.4465
PotEng = -7431.7912 E_bond = 110.5122 E_angle = 329.8173
E_dihed = 534.5353 E_impro = 5.5900 E_vdwl = 541.3805
E_coul = 24227.6695 E_long = -33181.2961 Press = -1628.5627
---------------- Step 900 ----- CPU = 5.7072 (sec) ----------------
TotEng = -6239.5270 KinEng = 1162.7914 Temp = 272.5378
PotEng = -7402.3184 E_bond = 104.9538 E_angle = 347.6531
E_dihed = 536.4713 E_impro = 4.6832 E_vdwl = 483.3306
E_coul = 24295.7423 E_long = -33175.1528 Press = -1959.1567
---------------- Step 1000 ----- CPU = 6.3345 (sec) ----------------
TotEng = -6239.5020 KinEng = 1128.3312 Temp = 264.4609
PotEng = -7367.8332 E_bond = 102.9814 E_angle = 352.0690
E_dihed = 540.5086 E_impro = 3.6712 E_vdwl = 495.7763
E_coul = 24316.4138 E_long = -33179.2534 Press = -1881.5655
Loop time of 6.33458 on 8 procs for 1000 steps with 1968 atoms
TotEng = -6345.9602 KinEng = 0.0000 Temp = 0.0000
PotEng = -6345.9602 E_bond = 118.9251 E_angle = 315.7533
E_dihed = 532.0702 E_impro = 3.4517 E_vdwl = -491.3979
E_coul = 26261.2546 E_long = -33086.0173 Press = -13274.6498
---------------- Step 100 ----- CPU = 1.5587 (sec) ----------------
TotEng = -6089.2059 KinEng = 737.9545 Temp = 172.9635
PotEng = -6827.1604 E_bond = 99.2610 E_angle = 293.4796
E_dihed = 518.3926 E_impro = 3.4260 E_vdwl = -53.1737
E_coul = 25455.9659 E_long = -33144.5118 Press = -7582.0585
---------------- Step 200 ----- CPU = 3.1808 (sec) ----------------
TotEng = -6089.3334 KinEng = 1048.0815 Temp = 245.6518
PotEng = -7137.4150 E_bond = 105.4181 E_angle = 314.1091
E_dihed = 525.7575 E_impro = 2.0633 E_vdwl = 549.1716
E_coul = 24511.2323 E_long = -33145.1669 Press = -1214.5095
---------------- Step 300 ----- CPU = 4.8699 (sec) ----------------
TotEng = -6089.3928 KinEng = 1163.3028 Temp = 272.6576
PotEng = -7252.6956 E_bond = 101.6270 E_angle = 351.8828
E_dihed = 525.2212 E_impro = 3.1286 E_vdwl = 516.2458
E_coul = 24404.4712 E_long = -33155.2722 Press = -2323.5317
---------------- Step 400 ----- CPU = 6.5652 (sec) ----------------
TotEng = -6089.4987 KinEng = 1182.3885 Temp = 277.1310
PotEng = -7271.8872 E_bond = 114.0720 E_angle = 325.6458
E_dihed = 516.7310 E_impro = 3.1876 E_vdwl = 522.6196
E_coul = 24402.0712 E_long = -33156.2144 Press = -2169.9377
---------------- Step 500 ----- CPU = 8.2547 (sec) ----------------
TotEng = -6089.4538 KinEng = 1158.7955 Temp = 271.6012
PotEng = -7248.2493 E_bond = 103.0865 E_angle = 339.1037
E_dihed = 522.7155 E_impro = 2.6322 E_vdwl = 439.8428
E_coul = 24513.5109 E_long = -33169.1409 Press = -1803.4201
---------------- Step 600 ----- CPU = 9.9107 (sec) ----------------
TotEng = -6089.5529 KinEng = 1205.1352 Temp = 282.4624
PotEng = -7294.6881 E_bond = 108.2588 E_angle = 346.6746
E_dihed = 531.5390 E_impro = 3.2909 E_vdwl = 459.2427
E_coul = 24426.5336 E_long = -33170.2276 Press = -2567.6797
---------------- Step 700 ----- CPU = 11.5432 (sec) ----------------
TotEng = -6089.5542 KinEng = 1192.6231 Temp = 279.5298
PotEng = -7282.1773 E_bond = 111.1701 E_angle = 368.3148
E_dihed = 531.3469 E_impro = 3.6338 E_vdwl = 526.5919
E_coul = 24341.9242 E_long = -33165.1590 Press = -1918.0534
---------------- Step 800 ----- CPU = 13.1827 (sec) ----------------
TotEng = -6089.6409 KinEng = 1211.1193 Temp = 283.8650
PotEng = -7300.7601 E_bond = 104.1488 E_angle = 343.9467
E_dihed = 536.0043 E_impro = 5.1288 E_vdwl = 507.6841
E_coul = 24380.9222 E_long = -33178.5951 Press = -1535.2124
---------------- Step 900 ----- CPU = 14.8342 (sec) ----------------
TotEng = -6089.6435 KinEng = 1219.9414 Temp = 285.9327
PotEng = -7309.5848 E_bond = 106.3702 E_angle = 362.6403
E_dihed = 531.9023 E_impro = 4.1736 E_vdwl = 532.4576
E_coul = 24326.4696 E_long = -33173.5985 Press = -694.2393
---------------- Step 1000 ----- CPU = 16.5041 (sec) ----------------
TotEng = -6089.6045 KinEng = 1204.4192 Temp = 282.2946
PotEng = -7294.0238 E_bond = 108.7432 E_angle = 365.2088
E_dihed = 541.1125 E_impro = 5.8781 E_vdwl = 533.2755
E_coul = 24329.0904 E_long = -33177.3322 Press = -1373.0623
Loop time of 16.5043 on 4 procs for 1000 steps with 1968 atoms
Performance: 13.639 ns/day, 1.760 hours/ns, 157.864 timesteps/s
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
Performance: 5.235 ns/day, 4.585 hours/ns, 60.590 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2335 | 2.5532 | 3.1707 | 18.5 | 40.31
Bond | 0.01158 | 0.051889 | 0.080867 | 9.9 | 0.82
Kspace | 2.1965 | 2.7773 | 3.0728 | 16.7 | 43.84
Neigh | 0.24407 | 0.24588 | 0.24863 | 0.3 | 3.88
Comm | 0.36894 | 0.37849 | 0.39142 | 1.3 | 5.97
Output | 0.0083764 | 0.0085732 | 0.0087767 | 0.1 | 0.14
Modify | 0.25864 | 0.28389 | 0.2976 | 2.5 | 4.48
Other | | 0.03539 | | | 0.56
Pair | 8.2128 | 9.5121 | 11.127 | 36.9 | 57.63
Bond | 0.035131 | 0.11618 | 0.15792 | 14.0 | 0.70
Kspace | 4.0276 | 5.4843 | 6.6741 | 44.1 | 33.23
Neigh | 0.66517 | 0.66553 | 0.66594 | 0.0 | 4.03
Comm | 0.28238 | 0.35525 | 0.41804 | 9.9 | 2.15
Output | 0.01374 | 0.014323 | 0.015721 | 0.7 | 0.09
Modify | 0.28166 | 0.28593 | 0.29397 | 0.9 | 1.73
Other | | 0.07076 | | | 0.43
Nlocal: 246 ave 290 max 210 min
Histogram: 1 1 0 1 2 0 2 0 0 1
Nghost: 6160.5 ave 6438 max 5877 min
Histogram: 2 0 0 1 0 2 0 1 1 1
Neighs: 116321 ave 144703 max 98946 min
Histogram: 1 2 1 1 0 2 0 0 0 1
Nlocal: 492 ave 517 max 456 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 7866 ave 8035 max 7664 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 232474 ave 255787 max 198462 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 930570
Ave neighs/atom = 472.851
Total # of neighbors = 929895
Ave neighs/atom = 472.508
Ave special neighs/atom = 4.4065
Neighbor list builds = 46
Neighbor list builds = 47
Dangerous builds = 0
Total wall time: 0:00:07
Total wall time: 0:00:18

1774
tools/ch2lmp/example/1ac7_ctrl.pdb
View File

File diff suppressed because it is too large Load Diff

1946
tools/ch2lmp/example/1ac7_ctrl.psf
View File

File diff suppressed because it is too large Load Diff

3
tools/ch2lmp/example/convert.sh Executable file
View File

@ -0,0 +1,3 @@
#!/bin/sh
rm -f 1ac7.restart* 1ac7.dump
../charmm2lammps.pl -water -ions -border=2.0 all27_na 1ac7

12
tools/ch2lmp/main_manual
View File

@ -1,12 +0,0 @@
The charmm2lmp sub-directory contains tools for converting files back-and-forth between
the CHARMM MD code and LAMMPS.
The charmm2lammps.pl perl script converts CHARMM input files into LAMMPS input.
The lammps2pdb.pl perl script converts LAMMPS dump files into a pdb series file.
The mkpdb.f fortran 90 code also converts LAMMPS dump files into PDB files, and the
mkdcd.f tool converts LAMMPS dump files into CHARMM *.dcd trajectory files that can
be read-in to CHARMM for analysis. See the README file in the charmm2lmp sub-directory
for more information.
These tools were written by Pieter J. in 't Veld (pjintve@sandia.gov) and Paul Crozier
(pscrozi@sandia.gov) at Sandia.