[gmx-users] segmentation fault in position restrained step
Moeed
lecielll at googlemail.com
Mon Apr 26 02:17:20 CEST 2010
Dear Justin,
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..
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?
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot
-0.18
2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot
-0.3
3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot
-0.42
4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot
-0.54
5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot
-0.66
6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot
-0.84
7 opls_140 1 HEX H1 1 0.06 1.008 ; qtot
-0.78
8 opls_140 1 HEX H2 1 0.06 1.008 ; qtot
-0.72
9 opls_140 1 HEX H3 1 0.06 1.008 ; qtot
-0.66
10 opls_140 1 HEX H4 2 0.06 1.008 ; qtot
-0.6
11 opls_140 1 HEX H5 2 0.06 1.008 ; qtot
-0.54
12 opls_140 1 HEX H6 3 0.06 1.008 ; qtot
-0.48
13 opls_140 1 HEX H7 3 0.06 1.008 ; qtot
-0.42
14 opls_140 1 HEX H8 4 0.06 1.008 ; qtot
-0.36
15 opls_140 1 HEX H9 4 0.06 1.008 ; qtot
-0.3
16 opls_140 1 HEX H10 5 0.06 1.008 ; qtot
-0.24
17 opls_140 1 HEX H11 5 0.06 1.008 ; qtot
-0.18
18 opls_140 1 HEX H12 6 0.06 1.008 ; qtot
-0.12
19 opls_140 1 HEX H13 6 0.06 1.008 ; qtot
-0.06
20 opls_140 1 HEX H14 6 0.06 1.008 ; qtot
0
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
http://oldwiki.gromacs.org/index.php/blowing_=upbut 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?
output.mdrun_pr
starting mdrun 'HEX'
500 steps, 1.0 ps.
^Mstep 0
Step 26, time 0.052 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000193, max 0.001508 (between atoms 81 and 100)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2541 2558 31.8 0.1090 0.1090 0.1090
Step 29, time 0.058 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000200, max 0.001497 (between atoms 1661 and 1678)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
301 318 31.4 0.1091 0.1090 0.1090
1521 1538 30.7 0.1091 0.1091 0.1090
Step 31, time 0.062 (ps) LINCS WARNING
relative constraint deviation after LINCS:rms 0.000184, max 0.001189
(between atoms 1582 and 1596)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
321 338 30.4 0.1091 0.1091 0.1090
1861 1878 31.4 0.1091 0.1090 0.1090
3481 3498 30.1 0.1091 0.1091 0.1090
4841 4858 30.3 0.1091 0.1091 0.1090
Step 33, time 0.066 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000191, max 0.001602 (between atoms 4542 and 4556)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3101 3118 30.5 0.1091 0.1091 0.1090
Step 38, time 0.076 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000242, max 0.001985 (between atoms 2885 and 2891)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2885 2891 33.2 0.1090 0.1092 0.1090
Step 39, time 0.078 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000234, max 0.002949 (between atoms 1465 and 1471)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1425 1431 33.6 0.1090 0.1092 0.1090
1465 1471 43.8 0.1090 0.1093 0.1090
1461 1478 30.2 0.1090 0.1091 0.1090
3005 3011 33.3 0.1090 0.1091 0.1090
3105 3111 40.4 0.1090 0.1093 0.1090
4025 4031 30.5 0.1090 0.1092 0.1090
4021 4038 33.0 0.1090 0.1092 0.1090
Step 40, time 0.08 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000231, max 0.006255 (between atoms 2865 and 2871)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
985 991 47.7 0.1090 0.1094 0.1090
981 998 33.5 0.1090 0.1092 0.1090
1585 1591 31.3 0.1090 0.1091 0.1090
2865 2871 64.9 0.1090 0.1097 0.1090
2861 2878 48.1 0.1090 0.1091 0.1090
3105 3111 34.3 0.1093 0.1091 0.1090
Step 41, time 0.082 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000219, max 0.005322 (between atoms 865 and 871)
bonds that rotated more than 30 degrees:bonds that rotated more than 30
degrees:
atom 1 atom 2 angle previous, current, constraint length
865 871 45.0 0.1096 0.1089 0.1090
986 988 38.0 0.1090 0.1091 0.1090
985 991 32.5 0.1090 0.1090 0.1090
1465 1471 47.9 0.1092 0.1090 0.1090
2005 2011 30.2 0.1090 0.1091 0.1090
2925 2931 90.0 0.1090 0.1141 0.1090
2921 2938 58.6 0.1090 0.1096 0.1090
Step 43, time 0.086 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056702, max 3.196747 (between atoms 2926 and 2928)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
865 871 62.8 0.1089 0.1078 0.1090
985 991 30.9 0.1090 0.1090 0.1090
1465 1471 43.5 0.1090 0.1091 0.1090
2926 2928 90.0 0.1091 0.4574 0.1090
2925 2931 89.9 0.1141 0.3619 0.1090
2921 2938 36.2 0.1096 0.1088 0.1090
3806 3808 90.0 0.1090 0.1291 0.1090
3805 3811 54.4 0.1090 0.1101 0.1090
Wrote pdb files with previous and current coordinates
Step 44, time 0.088 (ps) LINCS WARNING
atom 1 atom 2 angle previous, current, constraint length
relative constraint deviation after LINCS:
rms 0.010167, max 0.571986 (between atoms 1464 and 1472)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
865 871 51.9 0.1078 0.1095 0.1090
1465 1471 50.7 0.1091 0.1083 0.1090
1464 1472 90.0 0.1089 0.1713 0.1090
1461 1478 35.7 0.1090 0.1093 0.1090
2926 2928 46.8 0.4574 0.1044 0.1090
2925 2931 90.4 0.3619 0.1542 0.1090
3806 3808 60.1 0.1291 0.1076 0.1090
3805 3811 77.1 0.1101 0.1097 0.1090
Wrote pdb files with previous and current coordinates
Step 45, time 0.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.837736, max 51.641046 (between atoms 864 and 872)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
866 869 86.2 0.1090 0.0467 0.1090
866 867 85.4 0.1090 0.0505 0.1090
865 871 89.9 0.1095 3.0474 0.1090
865 870 82.2 0.1095 0.0570 0.1090
865 866 91.8 0.1533 0.1376 0.1530
864 873 88.7 0.1090 0.2586 0.1090
864 872 90.0 0.1090 5.7379 0.1090
864 865 87.9 0.1532 0.5058 0.1530
863 875 84.9 0.1090 0.2277 0.1090
863 874 55.9 0.1090 0.1560 0.1090
863 864 89.8 0.1540 0.3037 0.1540
862 863 60.9 0.1530 0.2445 0.1530
984 992 30.8 0.1090 0.1090 0.1090
1465 1471 58.3 0.1083 0.1108 0.1090
1464 1472 65.8 0.1713 0.1092 0.1090
1461 1478 32.4 0.1093 0.1092 0.1090
2926 2928 90.0 0.1044 0.3092 0.1090
2925 2931 90.1 0.1542 0.3747 0.1090
3806 3808 90.0 0.1076 0.1095 0.1090
3805 3811 42.8 0.1097 0.1090 0.1090
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 862 and 872 at distance 5.514 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 46, time 0.092 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 11.415864, max 784.685438 (between atoms 864 and 873)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
861 862 90.1 0.1572 7.2601 0.1530 866 869 88.9
0.0467 0.8828 0.1090
866 868 92.7 0.1000 0.8942 0.1090
866 867 89.3 0.0505 0.9796 0.1090
865 871 88.8 3.0474 3.4150 0.1090
865 870 87.8 0.0570 2.2657 0.1090
865 866 89.1 0.1376 2.0123 0.1530
864 873 89.8 0.2586 85.6397 0.1090
864 872 87.3 5.7379 2.9060 0.1090
864 865 80.4 0.5058 2.0822 0.1530
863 875 88.3 0.2277 1.2076 0.1090
863 874 91.2 0.1560 1.2040 0.1090
863 864 87.3 0.3037 4.2623 0.1540
862 877 90.0 0.1142 2.8762 0.1090
862 876 90.4 0.1107 2.6561 0.1090
862 863 88.2 0.2445 1.7121 0.1530
861 880 89.8 0.1118 5.4334 0.1090
861 879 90.0 0.1077 6.9930 0.1090
861 878 89.7 0.1083 2.0454 0.1090
985 990 30.4 0.1088 0.1090 0.1090
984 992 38.3 0.1090 0.1091 0.1090
983 995 47.6 0.1090 0.1091 0.1090
1466 1469 90.0 0.1088 0.1770 0.1090
1465 1471 90.1 0.1108 0.2046 0.1090
1464 1472 90.1 0.1092 0.1559 0.1090
2865 2870 34.3 0.1092 0.1091 0.1090
2926 2929 89.0 0.1099 0.3714 0.1090
2926 2928 90.1 0.3092 7.5029 0.1090
2926 2927 90.6 0.1095 0.3827 0.1090
2925 2931 92.0 0.3747 0.3177 0.1090
2925 2930 88.9 0.1093 0.2022 0.1090
2925 2926 92.2 0.1526 0.1868 0.1530
2924 2933 89.1 0.1090 0.3161 0.1090
2924 2932 89.9 0.1092 0.4603 0.1090
2924 2925 87.9 0.1518 0.6112 0.1530
2923 2935 88.8 0.1091 0.3420 0.1090
2923 2934 71.2 0.1089 0.1499 0.1090
2923 2924 90.7 0.1543 0.5792 0.1540
2922 2937 32.2 0.1090 0.1275 0.1090
2922 2923 70.5 0.1529 0.2721 0.1530
3806 3808 90.0 0.1095 0.1317 0.1090
3805 3811 41.9 0.1090 0.1099 0.1090
3804 3812 34.9 0.1090 0.1086 0.1090
Wrote pdb files with previous and current coordinates
********************************************************************************************************
I have written a new pr.mdp file for creating tpr file was:
;title =
cpp = /lib/cpp
; Preprocessing
define = -DPOSRES
; Run control
integrator = md
dt = 0.002 ; ps !
nsteps = 500 ; total 1.0 ps.
; Output control
nstenergy = 10 ; energies and other statistical data are
stored every 10 steps
; Neighbor searching
nstlist = 10 ; neighborlist will be updated at least
every 10 steps
;ns_type = grid
; Electrostatics/VdW
coulombtype = PME
vdw-type = cut-off
; Cut-off
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Temperature coupling: Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = HEX
tau_t = 0.1
ref_t = 300
; Pressure coupling: Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Velocity generation: Generate velocites is on at 300 K. Manual p155
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
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