Dear Justin,<br><br>1- Could you please check if I have grouped atoms properly? Lastly, I could generate the tpr file for PR step. Since I am getting segmentation fault in the next step I though maybe there is sth wring with charge groups.. <br>
<br>However, I have a funda,mental question. I am to compute interaction parameters for ternary system of hexane/polyethylene/ethylene. Sofar I have only hexane as solvent, later polyethylene and ethylene will be added. My questions is for this apolar system, do I need to worry about electrostatic interactions between atoms? I mean could I skip buildig charge groups if I am interested in cacluation of interaction parameters BETWEEN hexane, polyethylene and ethylene?<br>
<br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18<br> 2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.3<br>
3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.42<br> 4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.54<br> 5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.66<br>
6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.84<br> 7 opls_140 1 HEX H1 1 0.06 1.008 ; qtot -0.78<br> 8 opls_140 1 HEX H2 1 0.06 1.008 ; qtot -0.72<br>
9 opls_140 1 HEX H3 1 0.06 1.008 ; qtot -0.66<br> 10 opls_140 1 HEX H4 2 0.06 1.008 ; qtot -0.6<br> 11 opls_140 1 HEX H5 2 0.06 1.008 ; qtot -0.54<br>
12 opls_140 1 HEX H6 3 0.06 1.008 ; qtot -0.48<br> 13 opls_140 1 HEX H7 3 0.06 1.008 ; qtot -0.42<br> 14 opls_140 1 HEX H8 4 0.06 1.008 ; qtot -0.36<br>
15 opls_140 1 HEX H9 4 0.06 1.008 ; qtot -0.3<br> 16 opls_140 1 HEX H10 5 0.06 1.008 ; qtot -0.24<br> 17 opls_140 1 HEX H11 5 0.06 1.008 ; qtot -0.18<br>
18 opls_140 1 HEX H12 6 0.06 1.008 ; qtot -0.12<br> 19 opls_140 1 HEX H13 6 0.06 1.008 ; qtot -0.06<br> 20 opls_140 1 HEX H14 6 0.06 1.008 ; qtot 0<br>
<br>2- I tried to run the position restrained simulation. VERSION 4.0.7 with "mdrun -s Hexane_pr.tpr -o Hexane_pr.tpr -c Hexane_b4md -v >& output.mdrun_pr". After a few seconds I get segmentation fault error. I did a thorough search on mailing list and found a smilar situation where Mr. MArck Abraham introduced <a href="http://oldwiki.gromacs.org/index.php/blowing_=up">http://oldwiki.gromacs.org/index.php/blowing_=up</a> but link is not working. Do I need to change the constraint algorithm? Could you please tell me why I am getting segmentation error? Does it have to do with kinetic energy?<br>
<br>output.mdrun_pr<br><br>starting mdrun 'HEX'<br>500 steps, 1.0 ps.<br>^Mstep 0<br>Step 26, time 0.052 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000193, max 0.001508 (between atoms 81 and 100)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 2541 2558 31.8 0.1090 0.1090 0.1090<br><br>Step 29, time 0.058 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000200, max 0.001497 (between atoms 1661 and 1678)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 301 318 31.4 0.1091 0.1090 0.1090<br>
1521 1538 30.7 0.1091 0.1091 0.1090<br><br>Step 31, time 0.062 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:rms 0.000184, max 0.001189 (between atoms 1582 and 1596)<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 321 338 30.4 0.1091 0.1091 0.1090<br> 1861 1878 31.4 0.1091 0.1090 0.1090<br> 3481 3498 30.1 0.1091 0.1091 0.1090<br>
4841 4858 30.3 0.1091 0.1091 0.1090<br><br>Step 33, time 0.066 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000191, max 0.001602 (between atoms 4542 and 4556)<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 3101 3118 30.5 0.1091 0.1091 0.1090<br><br>Step 38, time 0.076 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000242, max 0.001985 (between atoms 2885 and 2891)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 2885 2891 33.2 0.1090 0.1092 0.1090<br><br>Step 39, time 0.078 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000234, max 0.002949 (between atoms 1465 and 1471)<br>bonds that rotated more than 30 degrees:<br>atom 1 atom 2 angle previous, current, constraint length<br> 1425 1431 33.6 0.1090 0.1092 0.1090<br>
1465 1471 43.8 0.1090 0.1093 0.1090<br> 1461 1478 30.2 0.1090 0.1091 0.1090<br> 3005 3011 33.3 0.1090 0.1091 0.1090<br> 3105 3111 40.4 0.1090 0.1093 0.1090<br>
4025 4031 30.5 0.1090 0.1092 0.1090<br> 4021 4038 33.0 0.1090 0.1092 0.1090<br><br>Step 40, time 0.08 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000231, max 0.006255 (between atoms 2865 and 2871)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 985 991 47.7 0.1090 0.1094 0.1090<br> 981 998 33.5 0.1090 0.1092 0.1090<br> 1585 1591 31.3 0.1090 0.1091 0.1090<br>
2865 2871 64.9 0.1090 0.1097 0.1090<br> 2861 2878 48.1 0.1090 0.1091 0.1090<br> 3105 3111 34.3 0.1093 0.1091 0.1090<br><br>Step 41, time 0.082 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000219, max 0.005322 (between atoms 865 and 871)<br>bonds that rotated more than 30 degrees:bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 865 871 45.0 0.1096 0.1089 0.1090<br>
986 988 38.0 0.1090 0.1091 0.1090<br> 985 991 32.5 0.1090 0.1090 0.1090<br> 1465 1471 47.9 0.1092 0.1090 0.1090<br> 2005 2011 30.2 0.1090 0.1091 0.1090<br>
2925 2931 90.0 0.1090 0.1141 0.1090<br> 2921 2938 58.6 0.1090 0.1096 0.1090<br><br>Step 43, time 0.086 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.056702, max 3.196747 (between atoms 2926 and 2928)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 865 871 62.8 0.1089 0.1078 0.1090<br> 985 991 30.9 0.1090 0.1090 0.1090<br> 1465 1471 43.5 0.1090 0.1091 0.1090<br>
2926 2928 90.0 0.1091 0.4574 0.1090<br> 2925 2931 89.9 0.1141 0.3619 0.1090<br> 2921 2938 36.2 0.1096 0.1088 0.1090<br> 3806 3808 90.0 0.1090 0.1291 0.1090<br>
3805 3811 54.4 0.1090 0.1101 0.1090<br>Wrote pdb files with previous and current coordinates<br><br>Step 44, time 0.088 (ps) LINCS WARNING<br><br> atom 1 atom 2 angle previous, current, constraint length<br>
relative constraint deviation after LINCS:<br>rms 0.010167, max 0.571986 (between atoms 1464 and 1472)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 865 871 51.9 0.1078 0.1095 0.1090<br>
1465 1471 50.7 0.1091 0.1083 0.1090<br> 1464 1472 90.0 0.1089 0.1713 0.1090<br> 1461 1478 35.7 0.1090 0.1093 0.1090<br> 2926 2928 46.8 0.4574 0.1044 0.1090<br>
2925 2931 90.4 0.3619 0.1542 0.1090<br> 3806 3808 60.1 0.1291 0.1076 0.1090<br> 3805 3811 77.1 0.1101 0.1097 0.1090<br>Wrote pdb files with previous and current coordinates<br>
<br>Step 45, time 0.09 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.837736, max 51.641046 (between atoms 864 and 872)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
866 869 86.2 0.1090 0.0467 0.1090<br> 866 867 85.4 0.1090 0.0505 0.1090<br> 865 871 89.9 0.1095 3.0474 0.1090<br> 865 870 82.2 0.1095 0.0570 0.1090<br>
865 866 91.8 0.1533 0.1376 0.1530<br> 864 873 88.7 0.1090 0.2586 0.1090<br> 864 872 90.0 0.1090 5.7379 0.1090<br> 864 865 87.9 0.1532 0.5058 0.1530<br>
863 875 84.9 0.1090 0.2277 0.1090<br> 863 874 55.9 0.1090 0.1560 0.1090<br> 863 864 89.8 0.1540 0.3037 0.1540<br> 862 863 60.9 0.1530 0.2445 0.1530<br>
984 992 30.8 0.1090 0.1090 0.1090<br> 1465 1471 58.3 0.1083 0.1108 0.1090<br> 1464 1472 65.8 0.1713 0.1092 0.1090<br> 1461 1478 32.4 0.1093 0.1092 0.1090<br>
2926 2928 90.0 0.1044 0.3092 0.1090<br> 2925 2931 90.1 0.1542 0.3747 0.1090<br> 3806 3808 90.0 0.1076 0.1095 0.1090<br> 3805 3811 42.8 0.1097 0.1090 0.1090<br>
Wrote pdb files with previous and current coordinates<br>Warning: 1-4 interaction between 862 and 872 at distance 5.514 which is larger than the 1-4 table size 2.000 nm<br>These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>Step 46, time 0.092 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 11.415864, max 784.685438 (between atoms 864 and 873)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 861 862 90.1 0.1572 7.2601 0.1530 866 869 88.9 0.0467 0.8828 0.1090<br>
866 868 92.7 0.1000 0.8942 0.1090<br> 866 867 89.3 0.0505 0.9796 0.1090<br> 865 871 88.8 3.0474 3.4150 0.1090<br> 865 870 87.8 0.0570 2.2657 0.1090<br>
865 866 89.1 0.1376 2.0123 0.1530<br> 864 873 89.8 0.2586 85.6397 0.1090<br> 864 872 87.3 5.7379 2.9060 0.1090<br> 864 865 80.4 0.5058 2.0822 0.1530<br>
863 875 88.3 0.2277 1.2076 0.1090<br> 863 874 91.2 0.1560 1.2040 0.1090<br> 863 864 87.3 0.3037 4.2623 0.1540<br> 862 877 90.0 0.1142 2.8762 0.1090<br>
862 876 90.4 0.1107 2.6561 0.1090<br> 862 863 88.2 0.2445 1.7121 0.1530<br> 861 880 89.8 0.1118 5.4334 0.1090<br> 861 879 90.0 0.1077 6.9930 0.1090<br>
861 878 89.7 0.1083 2.0454 0.1090<br> 985 990 30.4 0.1088 0.1090 0.1090<br> 984 992 38.3 0.1090 0.1091 0.1090<br> 983 995 47.6 0.1090 0.1091 0.1090<br>
1466 1469 90.0 0.1088 0.1770 0.1090<br> 1465 1471 90.1 0.1108 0.2046 0.1090<br> 1464 1472 90.1 0.1092 0.1559 0.1090<br> 2865 2870 34.3 0.1092 0.1091 0.1090<br>
2926 2929 89.0 0.1099 0.3714 0.1090<br> 2926 2928 90.1 0.3092 7.5029 0.1090<br> 2926 2927 90.6 0.1095 0.3827 0.1090<br> 2925 2931 92.0 0.3747 0.3177 0.1090<br>
2925 2930 88.9 0.1093 0.2022 0.1090<br> 2925 2926 92.2 0.1526 0.1868 0.1530<br> 2924 2933 89.1 0.1090 0.3161 0.1090<br> 2924 2932 89.9 0.1092 0.4603 0.1090<br>
2924 2925 87.9 0.1518 0.6112 0.1530<br> 2923 2935 88.8 0.1091 0.3420 0.1090<br> 2923 2934 71.2 0.1089 0.1499 0.1090<br> 2923 2924 90.7 0.1543 0.5792 0.1540<br>
2922 2937 32.2 0.1090 0.1275 0.1090<br> 2922 2923 70.5 0.1529 0.2721 0.1530<br> 3806 3808 90.0 0.1095 0.1317 0.1090<br> 3805 3811 41.9 0.1090 0.1099 0.1090<br>
3804 3812 34.9 0.1090 0.1086 0.1090<br>Wrote pdb files with previous and current coordinates<br><br>********************************************************************************************************<br>
I have written a new pr.mdp file for creating tpr file was:<br><br><br>;title =<br>cpp = /lib/cpp<br><br>; Preprocessing<br>define = -DPOSRES<br>; Run control<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 500 ; total 1.0 ps.<br>; Output control<br>nstenergy = 10 ; energies and other statistical data are stored every 10 steps<br>; Neighbor searching<br>
nstlist = 10 ; neighborlist will be updated at least every 10 steps<br>;ns_type = grid<br>; Electrostatics/VdW<br>coulombtype = PME<br>vdw-type = cut-off<br>; Cut-off<br>
rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br>; Temperature coupling: Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = HEX <br>
tau_t = 0.1 <br>ref_t = 300 <br>; Pressure coupling: Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
; Velocity generation: Generate velocites is on at 300 K. Manual p155<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>; Bonds<br>constraints = all-bonds<br><br><br>
<br><br><br>