[gmx-users] LINCS Warning with MDRUN - Segmentation Fault

Gaurav Chopra gauravchopra at gmail.com
Mon Apr 17 09:07:29 CEST 2006


Hi

I am getting the following error with mdrun. I have done a few things but
the system complains of 1-4 interactions and gives LINCS warning if the
constraints are not turned off in the mdp file. I also changed the fudgeQQ =
1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4
interaction table size error and then LINCS warning. The output of mdrun for
one of these peptides is as follows. I am working on normal mode decoys of
each peptide and many of the decoys have no problems with mdrun but some
gives this error and Segmentation Fault.

Please advice.

Gaurav

OUTPUT OF MDRUN

Reading file md_1dsl.cl_nH_tir_00710.H_bf.tpr, VERSION 3.3 (single
precision)

Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.096062 (between atoms 879 and 882) rms 0.005336
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in
water'
100000 steps,    200.0 ps.


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.048269 (between atoms 879 and 882) rms 0.002486
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    895    896   33.7    0.1090   0.1092      0.1090

Step 13, time 0.026 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001279 (between atoms 882 and 883) rms 0.000069
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    882    883   32.9    0.1011   0.1011      0.1010

Step 14, time 0.028 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001462 (between atoms 882 and 883) rms 0.000068
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    882    883   34.0    0.1011   0.1011      0.1010

Step 15, time 0.03 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001105 (between atoms 888 and 890) rms 0.000070
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    882    883   31.8    0.1011   0.1010      0.1010

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001912 (between atoms 888 and 890) rms 0.000096
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    882    883   31.2    0.1010   0.1008      0.1010

Step 20, time 0.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.700586 (between atoms 873 and 875) rms 0.023589
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    873    875   90.0    0.1091   0.1854      0.1090
    876    878   90.0    0.1090   0.1724      0.1090

Step 21, time 0.042 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 29473624.000000 (between atoms 873 and 875) rms 776989.562500
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    835    837   34.7    0.1335   0.1732      0.1335
    837    838   37.4    0.1010   0.1346      0.1010
    837    839  109.7    0.1449 692.1205      0.1449
    839    840  111.1    0.1090 692.1713      0.1090
    839    841  100.5    0.1529 692.0815      0.1529
    839    846  106.7    0.1522 1817.9144      0.1522
    841    842   41.8    0.1090   0.1504      0.1090
    841    843   41.9    0.1090   0.1508      0.1090
    841    844   37.8    0.1410   0.1823      0.1410
    846    847  104.8    0.1229 1896.3798      0.1229
    846    848  104.1    0.1335 13946.6553      0.1335
    848    849  102.0    0.1010 12523.5713      0.1010
    848    850   93.4    0.1449 32162.5566      0.1449
    850    851   92.5    0.1090 31577.1289      0.1090
    850    852   95.3    0.1529 35935.5234      0.1529
    850    867   95.0    0.1523 138461.0938      0.1522
    852    853   99.7    0.1090 6120.9419      0.1090
    852    854   96.8    0.1090 6488.6191      0.1090
    852    855  104.6    0.1510 6414.0713      0.1510
    855    856  113.0    0.1400 1370.1686      0.1400
    855    858  112.2    0.1400 1379.8882      0.1400
    856    857  122.2    0.1080 281.0437      0.1080
    856    860  121.8    0.1400 280.9830      0.1400
    858    859  117.1    0.1080 268.9571      0.1080
    858    862  121.6    0.1400 268.9104      0.1400
    860    861   31.6    0.1080   0.1373      0.1080
    862    863   35.4    0.1080   0.1427      0.1080
    867    868   90.7    0.1229 144391.0938      0.1229
    867    869   90.2    0.1335 291070.9688      0.1335
    869    870   90.3    0.1010 301462.5000      0.1010
    869    871   90.5    0.1450 352037.4375      0.1449
    871    872   91.2    0.1092 39090.6250      0.1090
    871    873   80.9    0.1534 224179.3750      0.1529
    871    891  105.9    0.1523 63050.6406      0.1522
    873    874   83.6    0.1106 194899.4531      0.1090
    873    875   89.0    0.1854 3212625.0000      0.1090
    873    876  110.5    0.1526 154736.1719      0.1529
    876    877   83.1    0.1104 96243.8906      0.1090
    876    878   62.5    0.1724 90734.6406      0.1090
    876    879   80.3    0.1534 125826.9609      0.1529
    879    880  103.7    0.1100 48631.2148      0.1090
    879    881  103.6    0.1093 48326.8906      0.1090
    879    882   87.6    0.1467 53880.1172      0.1463
    882    883  117.6    0.1009 388.4776      0.1010
    882    884  160.2    0.1339 765.5904      0.1340
    884    885   67.9    0.1340 475.1604      0.1340
    884    888   70.4    0.1339 475.1462      0.1340
    885    886   41.1    0.1010   0.1340      0.1010
    885    887   40.5    0.1010   0.1327      0.1010
    888    889   36.7    0.1011   0.1255      0.1010
    891    892   86.4    0.1230 26705.6504      0.1229
    891    893   70.7    0.1337 25659.6777      0.1335
    893    894   81.4    0.1010 5832.3770      0.1010
    893    895  101.2    0.1449 6486.8506      0.1449
    895    896   78.8    0.1090 3401.6624      0.1090
    895    897   70.5    0.1091 3321.8872      0.1090
    895    898   67.6    0.1523 3357.9832      0.1522
    898    899   53.8    0.1229 268.3385      0.1229
    898    900   63.5    0.1335 268.3486      0.1335
    900    901   38.8    0.1010   0.1384      0.1010
    900    902   38.0    0.1449   0.1905      0.1449
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