[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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