[gmx-users] Constraint causing system to explode
Warren Gallin
wgallin at ualberta.ca
Thu May 27 17:30:33 CEST 2010
Hi,
I am looking at the the free energy profile of end-to end distances of various peptides, but I am consistently getting a system blow-up when running simulations with that distance constrained by a type 2 constraint.
I run a simulation of the unconstrained peptide in a box of tip4p water, Na+ and Cl- ions, and it runs with no problem.
Then I grab a frame of that simulation in which the end-to-end distance is 0.8 nm (full frame including water) as a .gro file. Then I add a type 2 constraint between the N-terminal nitrogen atom and the C-terminal carboxyl carbon, create a new .tpr file using the revised topology and the already equilibrated frame as starting files and a .mdp file that now has the free_energy set to on, and then launch mdrun.
About 189 ps into the simulation I start getting warnings as follows, ultimately leading to blow-up and the run failing (fragment of error file output shown at end of message).
I am obviously missing something about how the constraint is handled. Is it possible that this is a problem that arises because of domain decomposition over multiple nodes, ir is there something more basic that needs to be dealt with when imposing a type 2 constraint?
Warren Gallin
Step 94636, time 189.272 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.041028, max 0.161215 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 94637, time 189.274 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018884, max 0.100333 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 94638, time 189.276 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.039664, max 0.168134 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 94639, time 189.278 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009052, max 0.046170 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 94640, time 189.28 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.010107, max 0.040597 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 114146, time 228.292 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018616, max 0.132800 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 114147, time 228.294 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.067800, max 0.404060 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 114148, time 228.296 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004950, max 0.032340 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 114149, time 228.298 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003656, max 0.020543 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139429, time 278.858 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023892, max 0.091259 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139430, time 278.86 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023116, max 0.102488 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139431, time 278.862 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.031945, max 0.132323 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139432, time 278.864 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023118, max 0.104278 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139433, time 278.866 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024565, max 0.101936 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139434, time 278.868 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013388, max 0.058925 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139435, time 278.87 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.010470, max 0.039065 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139485, time 278.97 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024798, max 0.093767 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139486, time 278.972 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013846, max 0.063915 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139487, time 278.974 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022224, max 0.083264 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139489, time 278.978 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013728, max 0.054726 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139765, time 279.53 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022985, max 0.094260 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139766, time 279.532 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.027589, max 0.106359 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139767, time 279.534 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.036811, max 0.150949 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139768, time 279.536 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038539, max 0.159720 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139769, time 279.538 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.044402, max 0.183484 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139770, time 279.54 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.030319, max 0.130937 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139771, time 279.542 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024896, max 0.101979 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139772, time 279.544 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.012074, max 0.045284 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139804, time 279.608 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.026141, max 0.096731 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139805, time 279.61 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.046881, max 0.209117 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 139806, time 279.612 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.135897, max 0.671451 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
217 219 35.1 0.1389 0.1155 0.1364
Wrote pdb files with previous and current coordinates
Step 139807, time 279.614 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.463807, max 1.907767 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
209 211 55.3 0.1670 0.1166 0.1449
211 213 148.7 0.1747 0.0823 0.1529
211 212 85.8 0.1276 0.1099 0.1090
213 216 34.5 0.1068 0.1849 0.1090
213 215 44.7 0.1068 0.1898 0.1090
213 214 50.3 0.1068 0.1903 0.1090
217 219 122.9 0.1155 0.2845 0.1364
217 218 145.2 0.1184 0.2374 0.1229
1 2 119.9 0.1198 0.1317 0.1010
1 3 102.4 0.1168 0.1491 0.1010
Wrote pdb files with previous and current coordinates
Step 139808, time 279.616 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 93.072600, max 331.147736 (between atoms 211 and 212)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
207 209 134.9 0.1663 0.8982 0.1335
Step 139808, time 279.616 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.160504, max 1.489376 (between atoms 192 and 194)
207 208 89.8 0.1183 0.4092 0.1229
Step 139808, time 279.616 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.232834, max 2.483075 (between atoms 15 and 17)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
17 19 38.8 0.1454 0.1983 0.1449
17 18 53.6 0.1017 0.1606 0.1010
15 17 77.2 0.1463 0.4650 0.1335
15 16 57.4 0.1395 0.3929 0.1229
4 15 122.5 0.1259 2.8674 0.1522
4 6 155.9 0.1402 3.1992 0.1529
6 9 32.6 0.1640 0.7894 0.1529
9 12 61.6 0.1519 0.2701 0.1522
9 11 87.3 0.1091 0.2224 0.1090
9 10 91.9 0.1091 0.1829 0.1090
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
209 211 144.0 0.1166 6.0995 0.1449
6 8 84.3 0.1171 0.8254 0.1090
6 7 68.4 0.1171 0.7727 0.1090
4 5 126.9 0.0834 2.9326 0.1090
1 2 49.4 0.1317 15.1656 0.1010
1 217 152.5 0.4099 36.3370 0.8000
19 34 30.9 0.1526 0.1806 0.1522
19 21 31.7 0.1533 0.1823 0.1529
19 20 37.4 0.1094 0.1377 0.1090
190 192 49.8 0.1334 0.2086 0.1335
209 210 125.4 0.1150 0.8657 0.1010
192 194 87.3 0.1460 0.3607 0.1449
211 213 75.1 0.0823 6.8803 0.1529
194 207 73.0 0.1476 0.4958 0.1522
211 212 71.3 0.1099 36.2041 0.1090
207 209 134.2 0.1663 0.8955 0.1335
213 216 33.0 0.1849 4.3498 0.1090
209 211 145.0 0.1166 6.1038 0.1449
213 215 39.4 0.1898 3.0901 0.1090
211 213 76.9 0.0823 6.8276 0.1529
213 214 163.0 0.1903 7.2370 0.1090
211 212 71.7 0.1099 36.1349 0.1090
219 220 48.2 0.1198 7.1210 0.0945
209 210 124.9 0.1150 0.8624 0.1010
194 207 72.8 0.1476 0.4986 0.1522
207 208 90.0 0.1183 0.4064 0.1229
194 196 87.3 0.1541 0.3852 0.1529
194 196 87.3 0.1541 0.3856 0.1529
194 195 86.2 0.1099 0.2236 0.1090
196 199 52.1 0.1528 0.2402 0.1529
192 194 87.3 0.1460 0.3604 0.1449
196 198 62.3 0.1090 0.2087 0.1090
192 193 51.8 0.1010 0.1612 0.1010
196 197 62.1 0.1089 0.2080 0.1090
190 192 49.8 0.1334 0.2086 0.1335
194 195 86.2 0.1099 0.2240 0.1090
196 199 52.1 0.1528 0.2402 0.1529
192 193 51.8 0.1010 0.1612 0.1010
196 198 62.3 0.1090 0.2087 0.1090
196 197 62.1 0.1089 0.2080 0.1090
1 2 49.6 0.1317 15.1150 0.1010
1 217 152.4 0.4099 36.1637 0.8000
4 15 122.4 0.1259 2.8527 0.1522
4 6 155.9 0.1402 3.1804 0.1529
4 5 126.9 0.0834 2.9170 0.1090
6 9 32.7 0.1640 0.7866 0.1529
6 8 84.3 0.1171 0.8203 0.1090
6 7 68.4 0.1171 0.7674 0.1090
9 12 61.0 0.1519 0.2740 0.1522
9 11 87.1 0.1091 0.2213 0.1090
9 10 91.6 0.1091 0.1804 0.1090
15 17 77.3 0.1463 0.4632 0.1335
17 19 38.8 0.1454 0.1983 0.1449
19 34 30.8 0.1526 0.1806 0.1522
19 21 31.7 0.1533 0.1823 0.1529
19 20 37.4 0.1094 0.1377 0.1090
17 18 53.6 0.1017 0.1606 0.1010
15 16 57.4 0.1395 0.3912 0.1229
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun-mpi, VERSION 4.0.7
Source code file: pme.c, line: 518
Fatal error:
6 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group
-------------------------------------------------------
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