Hi<br>
<br>
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 <span style="text-decoration: underline;">not turned off</span>
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.<br>
<br>
Please advice.<br>
<br>
Gaurav<br>
<br style="font-weight: bold;">
<span style="text-decoration: underline; font-weight: bold;">OUTPUT OF MDRUN<br>
<span style="text-decoration: underline;"><span style="font-weight: bold;"><br>
</span></span></span><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;">Reading file md_1dsl.cl_nH_tir_00710.H_bf.tpr, VERSION 3.3 (single precision)<br>
<br>
Step -2, time -0.004 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.096062 (between atoms 879 and 882) rms 0.005336<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
starting mdrun 'Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water'<br>
100000 steps, 200.0 ps.<br>
<br>
<br>
Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.048269 (between atoms 879 and 882) rms 0.002486<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
895 896
33.7 0.1090
0.1092 0.1090<br>
<br>
Step 13, time 0.026 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.001279 (between atoms 882 and 883) rms 0.000069<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
882 883
32.9 0.1011
0.1011 0.1010<br>
<br>
Step 14, time 0.028 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.001462 (between atoms 882 and 883) rms 0.000068<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
882 883
34.0 0.1011
0.1011 0.1010<br>
<br>
Step 15, time 0.03 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.001105 (between atoms 888 and 890) rms 0.000070<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
882 883
31.8 0.1011
0.1010 0.1010<br>
<br>
Step 16, time 0.032 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.001912 (between atoms 888 and 890) rms 0.000096<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
882 883
31.2 0.1010
0.1008 0.1010<br>
<br>
Step 20, time 0.04 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.700586 (between atoms 873 and 875) rms 0.023589<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
873 875
90.0 0.1091
0.1854 0.1090<br>
876 878
90.0 0.1090
0.1724 0.1090<br>
<br>
Step 21, time 0.042 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 29473624.000000 (between atoms 873 and 875) rms 776989.562500<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
835 837
34.7 0.1335
0.1732 0.1335<br>
837 838
37.4 0.1010
0.1346 0.1010<br>
837 839 109.7 0.1449 692.1205 0.1449<br>
839 840 111.1 0.1090 692.1713 0.1090<br>
839 841 100.5 0.1529 692.0815 0.1529<br>
839 846 106.7 0.1522 1817.9144 0.1522<br>
841 842
41.8 0.1090
0.1504 0.1090<br>
841 843
41.9 0.1090
0.1508 0.1090<br>
841 844
37.8 0.1410
0.1823 0.1410<br>
846 847 104.8 0.1229 1896.3798 0.1229<br>
846 848
104.1 0.1335 13946.6553
0.1335<br>
848 849
102.0 0.1010 12523.5713
0.1010<br>
848 850
93.4 0.1449 32162.5566
0.1449<br>
850 851
92.5 0.1090 31577.1289
0.1090<br>
850 852
95.3 0.1529 35935.5234
0.1529<br>
850 867
95.0 0.1523 138461.0938
0.1522<br>
852 853
99.7 0.1090 6120.9419
0.1090<br>
852 854
96.8 0.1090 6488.6191
0.1090<br>
852 855 104.6 0.1510 6414.0713 0.1510<br>
855 856 113.0 0.1400 1370.1686 0.1400<br>
855 858 112.2 0.1400 1379.8882 0.1400<br>
856 857 122.2 0.1080 281.0437 0.1080<br>
856 860 121.8 0.1400 280.9830 0.1400<br>
858 859 117.1 0.1080 268.9571 0.1080<br>
858 862 121.6 0.1400 268.9104 0.1400<br>
860 861
31.6 0.1080
0.1373 0.1080<br>
862 863
35.4 0.1080
0.1427 0.1080<br>
867 868
90.7 0.1229 144391.0938
0.1229<br>
867 869
90.2 0.1335 291070.9688
0.1335<br>
869 870
90.3 0.1010 301462.5000
0.1010<br>
869 871
90.5 0.1450 352037.4375
0.1449<br>
871 872
91.2 0.1092 39090.6250
0.1090<br>
871 873
80.9 0.1534 224179.3750
0.1529<br>
871 891
105.9 0.1523 63050.6406
0.1522<br>
873 874
83.6 0.1106 194899.4531
0.1090<br>
873 875
89.0 0.1854
3212625.0000 0.1090<br>
873 876
110.5 0.1526
154736.1719 0.1529<br>
876 877
83.1 0.1104 96243.8906
0.1090<br>
876 878
62.5 0.1724 90734.6406
0.1090<br>
876 879
80.3 0.1534 125826.9609
0.1529<br>
879 880
103.7 0.1100 48631.2148
0.1090<br>
879 881
103.6 0.1093 48326.8906
0.1090<br>
879 882
87.6 0.1467 53880.1172
0.1463<br>
882 883 117.6 0.1009 388.4776 0.1010<br>
882 884 160.2 0.1339 765.5904 0.1340<br>
884 885
67.9 0.1340 475.1604
0.1340<br>
884 888
70.4 0.1339 475.1462
0.1340<br>
885 886
41.1 0.1010
0.1340 0.1010<br>
885 887
40.5 0.1010
0.1327 0.1010<br>
888 889
36.7 0.1011
0.1255 0.1010<br>
891 892
86.4 0.1230 26705.6504
0.1229<br>
891 893
70.7 0.1337 25659.6777
0.1335<br>
893 894
81.4 0.1010 5832.3770
0.1010<br>
893 895 101.2 0.1449 6486.8506 0.1449<br>
895 896
78.8 0.1090 3401.6624
0.1090<br>
895 897
70.5 0.1091 3321.8872
0.1090<br>
895 898
67.6 0.1523 3357.9832
0.1522<br>
898 899
53.8 0.1229 268.3385
0.1229<br>
898 900
63.5 0.1335 268.3486
0.1335<br>
900 901
38.8 0.1010
0.1384 0.1010<br>
900 902
38.0 0.1449
0.1905 0.1449</span></span></span><span style="text-decoration: underline; font-weight: bold;"><span style="text-decoration: underline;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="text-decoration: underline;">
<br>
</span></span><br>
<br>
</span></span><br>
</span>