[gmx-users] core dumped during equilibration in gromacs

ISHRAT JAHAN jishrat17 at gmail.com
Tue Apr 18 06:52:29 CEST 2017


Dear all,
I am trying to simulate protein  in urea box using "amber99sb-ildn" force
field.During the equilibration following error occur-Step 8, time 0.016
(ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000527 (between atoms 2089 and 2094)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   32.3    0.1010   0.1010      0.1010

Step 9, time 0.018 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000045, max 0.001791 (between atoms 2094 and 2096)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   31.6    0.1010   0.1008      0.1010

Step 10, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000042, max 0.001334 (between atoms 2094 and 2096)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   31.4    0.1008   0.1009      0.1010

Step 11, time 0.022 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000414, max 0.019232 (between atoms 2211 and 2213)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   31.8    0.1009   0.1010      0.1010
   2211   2213   89.9    0.1010   0.1029      0.1010

Step 12, time 0.024 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.019085, max 0.929098 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   31.7    0.1010   0.1011      0.1010
   2211   2213   80.4    0.1029   0.1011      0.1010
   2334   2336   34.5    0.1010   0.1010      0.1010
   2390   2392   90.0    0.1010   0.1948      0.1010

Back Off! I just backed up step12b.pdb to ./#step12b.pdb.5#

Back Off! I just backed up step12c.pdb to ./#step12c.pdb.5#
Wrote pdb files with previous and current coordinates

Step 13, time 0.026 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006403, max 0.311412 (between atoms 2251 and 2253)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.3    0.1011   0.1011      0.1010
   2211   2213   89.9    0.1011   0.1018      0.1010
   2251   2253   90.0    0.1010   0.1325      0.1010
   2334   2336   33.1    0.1010   0.1008      0.1010
   2390   2392   83.1    0.1948   0.1014      0.1010

Step 14, time 0.028 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022359, max 1.088377 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.3    0.1011   0.1010      0.1010
   2211   2213   90.0    0.1018   0.1025      0.1010
   2251   2253   79.0    0.1325   0.1012      0.1010
   2334   2336   31.7    0.1008   0.1009      0.1010
   2390   2392   90.0    0.1014   0.2109      0.1010

Back Off! I just backed up step14b.pdb to ./#step14b.pdb.3#

Back Off! I just backed up step14c.pdb to ./#step14c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 15, time 0.03 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004396, max 0.211385 (between atoms 2251 and 2253)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.8    0.1010   0.1009      0.1010
   2211   2213   56.5    0.1025   0.1010      0.1010
   2251   2253   90.0    0.1012   0.1223      0.1010
   2334   2336   30.8    0.1009   0.1011      0.1010
   2390   2392   90.0    0.2109   0.1041      0.1010

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022002, max 1.071041 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   32.0    0.1009   0.1009      0.1010
   2211   2213   56.4    0.1010   0.1003      0.1010
   2251   2253   90.0    0.1223   0.1015      0.1010
   2334   2336   30.7    0.1011   0.1011      0.1010
   2390   2392   89.9    0.1041   0.2092      0.1010

Back Off! I just backed up step16b.pdb to ./#step16b.pdb.3#

Back Off! I just backed up step16c.pdb to ./#step16c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 17, time 0.034 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003338, max 0.147245 (between atoms 2251 and 2253)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   33.3    0.1009   0.1011      0.1010
   2158   2160   35.6    0.1010   0.1010      0.1010
   2211   2213   56.4    0.1003   0.1015      0.1010
   2251   2253   89.9    0.1015   0.1159      0.1010
   2334   2336   33.4    0.1011   0.1010      0.1010
   2390   2392   90.0    0.2092   0.1079      0.1010

Step 18, time 0.036 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020801, max 1.012618 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   34.4    0.1011   0.1012      0.1010
   2158   2160   36.6    0.1010   0.1007      0.1010
   2211   2213   53.9    0.1015   0.1012      0.1010
   2251   2253   84.3    0.1159   0.1012      0.1010
   2334   2336   34.5    0.1010   0.1009      0.1010
   2390   2392   90.0    0.1079   0.2033      0.1010

Back Off! I just backed up step18b.pdb to ./#step18b.pdb.3#

Back Off! I just backed up step18c.pdb to ./#step18c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 19, time 0.038 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005936, max 0.245155 (between atoms 2126 and 2127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   31.3    0.1012   0.1011      0.1010
   2126   2127   90.0    0.1010   0.1258      0.1010
   2158   2160   37.3    0.1007   0.1009      0.1010
   2211   2213   52.9    0.1012   0.1004      0.1010
   2251   2253   90.0    0.1012   0.1021      0.1010
   2334   2336   35.3    0.1009   0.1009      0.1010
   2390   2392   90.0    0.2033   0.1163      0.1010

Step 20, time 0.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.019567, max 0.952451 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   32.1    0.1011   0.1009      0.1010
   2126   2127   75.9    0.1258   0.1010      0.1010
   2158   2160   38.0    0.1009   0.1013      0.1010
   2211   2213   56.5    0.1004   0.1012      0.1010
   2251   2253   90.0    0.1021   0.1023      0.1010
   2334   2336   35.9    0.1009   0.1011      0.1010
   2390   2392   89.9    0.1163   0.1972      0.1010

Back Off! I just backed up step20b.pdb to ./#step20b.pdb.3#

Back Off! I just backed up step20c.pdb to ./#step20c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 21, time 0.042 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002521, max 0.116842 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.2    0.1009   0.1009      0.1010
   2123   2124   37.8    0.1010   0.1006      0.1010
   2126   2127   90.1    0.1010   0.1046      0.1010
   2158   2160   40.4    0.1013   0.1013      0.1010
   2211   2213   54.5    0.1012   0.1016      0.1010
   2251   2253   64.2    0.1023   0.1009      0.1010
   2334   2336   34.9    0.1011   0.1013      0.1010
   2390   2392   90.1    0.1972   0.1128      0.1010

Step 22, time 0.044 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018059, max 0.878624 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.6    0.1009   0.1009      0.1010
   2123   2124   36.1    0.1006   0.1004      0.1010
   2126   2127   90.0    0.1046   0.1037      0.1010
   2158   2160   39.7    0.1013   0.1007      0.1010
   2211   2213   53.5    0.1016   0.1003      0.1010
   2251   2253   62.7    0.1009   0.1002      0.1010
   2334   2336   38.4    0.1013   0.1011      0.1010
   2390   2392   90.0    0.1128   0.1897      0.1010

Back Off! I just backed up step22b.pdb to ./#step22b.pdb.3#

Back Off! I just backed up step22c.pdb to ./#step22c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 23, time 0.046 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005118, max 0.236688 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.6    0.1009   0.1010      0.1010
   2123   2124   31.2    0.1004   0.0995      0.1010
   2126   2127   89.9    0.1037   0.1086      0.1010
   2158   2160   38.4    0.1007   0.1008      0.1010
   2211   2213   53.5    0.1003   0.1008      0.1010
   2251   2253   62.0    0.1002   0.1019      0.1010
   2334   2336   37.4    0.1011   0.1007      0.1010
   2390   2392   90.0    0.1897   0.1249      0.1010

Step 24, time 0.048 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016837, max 0.819486 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2126   2127   90.0    0.1086   0.1023      0.1010
   2158   2160   37.8    0.1008   0.1010      0.1010
   2211   2213   52.8    0.1008   0.1016      0.1010
   2251   2253   58.7    0.1019   0.1007      0.1010
   2334   2336   36.2    0.1007   0.1008      0.1010
   2390   2392   90.0    0.1249   0.1838      0.1010

Back Off! I just backed up step24b.pdb to ./#step24b.pdb.3#

Back Off! I just backed up step24c.pdb to ./#step24c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 25, time 0.05 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005570, max 0.256892 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2126   2127   89.9    0.1023   0.1097      0.1010
   2158   2160   36.9    0.1010   0.1011      0.1010
   2211   2213   54.9    0.1016   0.1009      0.1010
   2251   2253   60.8    0.1007   0.1004      0.1010
   2334   2336   34.9    0.1008   0.1011      0.1010
   2390   2392   90.0    0.1838   0.1269      0.1010

Step 26, time 0.052 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.014557, max 0.706394 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2126   2127   90.0    0.1097   0.1065      0.1010
   2158   2160   36.3    0.1011   0.1010      0.1010
   2211   2213   55.9    0.1009   0.1003      0.1010
   2251   2253   64.3    0.1004   0.1021      0.1010
   2334   2336   34.1    0.1011   0.1012      0.1010
   2390   2392   90.0    0.1269   0.1723      0.1010

Back Off! I just backed up step26b.pdb to ./#step26b.pdb.3#

Back Off! I just backed up step26c.pdb to ./#step26c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 27, time 0.054 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006686, max 0.319495 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2126   2127   89.9    0.1065   0.1072      0.1010
   2158   2160   37.6    0.1010   0.1008      0.1010
   2211   2213   58.5    0.1003   0.1017      0.1010
   2251   2253   62.7    0.1021   0.1004      0.1010
   2334   2336   31.8    0.1012   0.1010      0.1010
   2390   2392   90.1    0.1723   0.1333      0.1010

Step 28, time 0.056 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013884, max 0.675418 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2126   2127   90.0    0.1072   0.1035      0.1010
   2158   2160   38.2    0.1008   0.1008      0.1010
   2211   2213   48.9    0.1017   0.1011      0.1010
   2251   2253   62.0    0.1004   0.1007      0.1010
   2334   2336   31.3    0.1010   0.1009      0.1010
   2390   2392   90.0    0.1333   0.1692      0.1010

Back Off! I just backed up step28b.pdb to ./#step28b.pdb.3#

Back Off! I just backed up step28c.pdb to ./#step28c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 29, time 0.058 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006736, max 0.312627 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.4    0.1010   0.1011      0.1010
   2126   2127   90.0    0.1035   0.1109      0.1010
   2158   2160   39.4    0.1008   0.1012      0.1010
   2211   2213   48.1    0.1011   0.1004      0.1010
   2251   2253   60.3    0.1007   0.1019      0.1010
   2334   2336   32.5    0.1009   0.1010      0.1010
   2390   2392   90.3    0.1692   0.1326      0.1010

Step 30, time 0.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009507, max 0.458278 (between atoms 2387 and 2389)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2094   2096   30.2    0.1011   0.1011      0.1010
   2123   2124   30.8    0.1007   0.1013      0.1010
   2126   2127   90.0    0.1109   0.1070      0.1010
   2158   2160   40.4    0.1012   0.1014      0.1010
   2211   2213   47.9    0.1004   0.1010      0.1010
   2251   2253   57.3    0.1019   0.1004      0.1010
   2334   2336   33.8    0.1010   0.1012      0.1010
   2387   2388   30.2    0.1011   0.1025      0.1010
   2387   2389   90.2    0.1012   0.1473      0.1010
   2390   2392   76.0    0.1326   0.1012      0.1010

Step 31, time 0.062 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005728, max 0.277854 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2126   2127   90.0    0.1070   0.1020      0.1010
   2158   2160   31.5    0.1014   0.1010      0.1010
   2211   2213   43.7    0.1010   0.1013      0.1010
   2251   2253   55.2    0.1004   0.1007      0.1010
   2334   2336   32.9    0.1012   0.1012      0.1010
   2387   2389   44.9    0.1473   0.1003      0.1010
   2390   2392   90.2    0.1012   0.1291      0.1010

Step 32, time 0.064 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001969, max 0.073065 (between atoms 2387 and 2389)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2123   2124   37.5    0.1012   0.1010      0.1010
   2126   2127   90.0    0.1020   0.1057      0.1010
   2158   2160   31.2    0.1010   0.1009      0.1010
   2211   2213   42.7    0.1013   0.1009      0.1010
   2251   2253   57.7    0.1007   0.1020      0.1010
   2334   2336   30.5    0.1012   0.1010      0.1010
   2387   2389   90.5    0.1003   0.1084      0.1010
   2390   2392   86.4    0.1291   0.1015      0.1010

Step 33, time 0.066 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006294, max 0.304247 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2123   2124   35.7    0.1010   0.1008      0.1010
   2126   2127   85.7    0.1057   0.1002      0.1010
   2158   2160   30.7    0.1009   0.1008      0.1010
   2190   2191   33.3    0.1011   0.1011      0.1010
   2211   2213   44.1    0.1009   0.1007      0.1010
   2251   2253   58.7    0.1020   0.1004      0.1010
   2334   2336   30.3    0.1010   0.1008      0.1010
   2387   2389   76.9    0.1084   0.0993      0.1010
   2390   2392   89.9    0.1015   0.1317      0.1010

Step 34, time 0.068 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 133.867793, max 4615.651855 (between atoms 2387 and 2389)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2035   2037   48.7    0.1010   0.1010      0.1010
   2123   2124   35.1    0.1008   0.1008      0.1010
   2126   2127   90.0    0.1002   0.1088      0.1010
   2190   2191   30.6    0.1011   0.1009      0.1010
   2211   2213   45.7    0.1007   0.1010      0.1010
   2251   2253   58.1    0.1004   0.1005      0.1010
   2385   2386   56.8    0.1213   0.0892      0.1229
   2385   2387   99.7    0.1317   0.2141      0.1335
   2385   2390   97.5    0.1316   0.3057      0.1335
   2387   2388   94.8    0.1012   0.2607      0.1010
   2387   2389   88.7    0.0993 466.2818      0.1010
   2390   2391   85.9    0.1029   0.2297      0.1010
   2390   2392  119.4    0.1317 464.7838      0.1010

Back Off! I just backed up step34b.pdb to ./#step34b.pdb.3#

Back Off! I just backed up step34c.pdb to ./#step34c.pdb.3#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
Please help me  in solving above problem.
Thanks in advance.


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