[gmx-users] Re: simulation crash with GROMOS96 force field
Vitaly V. Chaban
vvchaban at gmail.com
Sun Jan 24 19:03:19 CET 2010
Hi Chris,
> 1. Is your system is properly minimized
Of course, it is, based on the energy values.
> 2. If you take the output from a 500 ps run with 0.25 fs timestep and
> start a 1 fs timestep run, is that new run stable?
Unfortunately the new run also crashes. The crash may be at the very
end while all the run goes well.
> 3. What are atoms 62 and 80?
These are non-bonded carbon and hydrogen of the same molecule.
> **4. Why is there a 1-4 between atoms 62 and 80 if you have only water
> and a 42 atom solute?
Because I have a number of solute molecules.
> 5. What does your .top look like? (does it list the organic molecule
> only once in the [ molecules ] section?)
Only once.
> 6. Do you have a bond or angle with a massive force constant that
> should indeed necessitate the small timestep for stability?
I think no... It look very strange for me that the run can be OK
during 500 ps but then unexpectedly crashes with producing PDB files
and similar messages about 1-4 interactions. Visualizing the dynamics
I do not notice anything strange - the molecule bends and oscillates
like any other does.
Thanks,
Vitaly
P.S. I list the topology generated by X2TOP below.
[ moleculetype ]
CIP 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 C 1 CIP C 9 0.221961 12.01115
2 C 1 CIP C 11 0.055382 12.01115
3 C 1 CIP C 10 -0.089181 12.01115
4 C 1 CIP C 8 -0.194750 12.01115
5 C 1 CIP C 7 -0.130399 12.01115
6 C 1 CIP C 7 -0.041791 12.01115
7 N 1 CIP N 6 0.063498 14.0067
8 C 1 CIP C 3 -0.117160 12.01115
9 C 1 CIP C 3 -0.177274 12.01115
10 C 1 CIP C 2 0.545958 12.01115
11 O 1 CIP O 2 -0.663625 15.9994
12 C 1 CIP C 1 0.656204 12.01115
13 O 1 CIP O 1 -0.574855 15.9994
14 O 1 CIP O 1 -0.631961 15.9994
15 F 1 CIP F 9 -0.243679 12.01115
16 N 1 CIP N 11 -0.111246 14.0067
17 C 1 CIP C 6 0.306136 12.01115
18 C 1 CIP C 4 0.043211 12.01115
19 C 1 CIP C 5 -0.718730 12.01115
20 C 1 CIP C 12 0.055448 12.01115
21 C 1 CIP C 14 0.145614 12.01115
22 N 1 CIP N 15 -0.832260 14.0067
23 C 1 CIP C 16 0.169804 12.01115
24 C 1 CIP C 13 -0.169448 12.01115
25 H 1 CIP H 10 0.034855 1.00797
26 H 1 CIP H 8 0.182392 1.00797
27 H 1 CIP H 3 0.180033 1.00797
28 H 1 CIP H 1 0.434432 1.00797
29 H 1 CIP H 6 0.039190 1.00797
30 H 1 CIP H 4 0.069751 1.00797
31 H 1 CIP H 4 0.065460 1.00797
32 H 1 CIP H 5 0.261152 1.00797
33 H 1 CIP H 5 0.244063 1.00797
34 H 1 CIP H 12 0.065977 1.00797
35 H 1 CIP H 12 0.013564 1.00797
36 H 1 CIP H 14 0.056687 1.00797
37 H 1 CIP H 14 0.054216 1.00797
38 H 1 CIP H 15 0.394600 1.00797
39 H 1 CIP H 16 0.059893 1.00797
40 H 1 CIP H 16 0.036976 1.00797
41 H 1 CIP H 13 0.109269 1.00797
42 H 1 CIP H 13 0.130633 1.00797
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.400000e-01 4.000000e+05 1.400000e-01
4.000000e+05
1 4 1 1.360000e-01 4.000000e+05 1.360000e-01
4.000000e+05
1 15 1 1.330000e-01 4.000000e+05 1.330000e-01
4.000000e+05
2 3 1 1.390000e-01 4.000000e+05 1.390000e-01
4.000000e+05
2 16 1 1.400000e-01 4.000000e+05 1.400000e-01
4.000000e+05
3 6 1 1.390000e-01 4.000000e+05 1.390000e-01
4.000000e+05
3 25 1 1.070000e-01 4.000000e+05 1.070000e-01
4.000000e+05
4 5 1 1.390000e-01 4.000000e+05 1.390000e-01
4.000000e+05
4 26 1 1.070000e-01 4.000000e+05 1.070000e-01
4.000000e+05
5 6 1 1.400000e-01 4.000000e+05 1.400000e-01
4.000000e+05
5 10 1 1.470000e-01 4.000000e+05 1.470000e-01
4.000000e+05
6 7 1 1.400000e-01 4.000000e+05 1.400000e-01
4.000000e+05
7 8 1 1.340000e-01 4.000000e+05 1.340000e-01
4.000000e+05
7 17 1 1.440000e-01 4.000000e+05 1.440000e-01
4.000000e+05
8 9 1 1.350000e-01 4.000000e+05 1.350000e-01
4.000000e+05
8 27 1 1.070000e-01 4.000000e+05 1.070000e-01
4.000000e+05
9 10 1 1.450000e-01 4.000000e+05 1.450000e-01
4.000000e+05
9 12 1 1.490000e-01 4.000000e+05 1.490000e-01
4.000000e+05
10 11 1 1.220000e-01 4.000000e+05 1.220000e-01
4.000000e+05
12 13 1 1.310000e-01 4.000000e+05 1.310000e-01
4.000000e+05
12 14 1 1.190000e-01 4.000000e+05 1.190000e-01
4.000000e+05
13 28 1 9.610000e-02 8.000000e+05 9.610000e-02
4.000000e+05
16 20 1 1.460000e-01 4.000000e+05 1.460000e-01
4.000000e+05
16 24 1 1.460000e-01 4.000000e+05 1.460000e-01
4.000000e+05
17 18 1 1.500000e-01 4.000000e+05 1.500000e-01
4.000000e+05
17 19 1 1.500000e-01 4.000000e+05 1.500000e-01
4.000000e+05
17 29 1 1.080000e-01 4.000000e+05 1.080000e-01
4.000000e+05
18 19 1 1.490000e-01 4.000000e+05 1.490000e-01
4.000000e+05
18 30 1 1.080000e-01 4.000000e+05 1.080000e-01
4.000000e+05
18 31 1 1.070000e-01 4.000000e+05 1.070000e-01
4.000000e+05
19 32 1 1.070000e-01 4.000000e+05 1.070000e-01
4.000000e+05
19 33 1 1.080000e-01 4.000000e+05 1.080000e-01
4.000000e+05
20 21 1 1.530000e-01 4.000000e+05 1.530000e-01
4.000000e+05
20 34 1 1.090000e-01 4.000000e+05 1.090000e-01
4.000000e+05
20 35 1 1.080000e-01 4.000000e+05 1.080000e-01
4.000000e+05
21 22 1 1.450000e-01 4.000000e+05 1.450000e-01
4.000000e+05
21 36 1 1.080000e-01 4.000000e+05 1.080000e-01
4.000000e+05
21 37 1 1.090000e-01 4.000000e+05 1.090000e-01
4.000000e+05
22 23 1 1.450000e-01 4.000000e+05 1.450000e-01
4.000000e+05
22 38 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05
23 24 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
23 39 1 1.080000e-01 4.000000e+05 1.080000e-01 4.000000e+05
23 40 1 1.080000e-01 4.000000e+05 1.080000e-01 4.000000e+05
24 41 1 1.080000e-01 4.000000e+05 1.080000e-01 4.000000e+05
24 42 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 6 1
1 10 1
1 20 1
1 24 1
1 25 1
2 5 1
2 7 1
2 21 1
2 23 1
2 26 1
2 34 1
2 35 1
2 41 1
2 42 1
3 4 1
3 8 1
3 10 1
3 15 1
3 17 1
3 20 1
3 24 1
4 7 1
4 9 1
4 11 1
4 16 1
5 8 1
5 12 1
5 15 1
5 17 1
5 25 1
6 9 1
6 11 1
6 16 1
6 18 1
6 19 1
6 26 1
6 27 1
6 29 1
7 10 1
7 12 1
7 25 1
7 30 1
7 31 1
7 32 1
7 33 1
8 11 1
8 13 1
8 14 1
8 18 1
8 19 1
8 29 1
9 17 1
9 28 1
10 13 1
10 14 1
10 26 1
10 27 1
11 12 1
12 27 1
14 28 1
15 16 1
15 26 1
16 22 1
16 25 1
16 36 1
16 37 1
16 39 1
16 40 1
17 27 1
20 23 1
20 38 1
20 41 1
20 42 1
21 24 1
21 39 1
21 40 1
22 34 1
22 35 1
22 41 1
22 42 1
23 36 1
23 37 1
24 34 1
24 35 1
24 38 1
29 30 1
29 31 1
29 32 1
29 33 1
30 32 1
30 33 1
31 32 1
31 33 1
34 36 1
34 37 1
35 36 1
35 37 1
36 38 1
37 38 1
38 39 1
38 40 1
39 41 1
39 42 1
40 41 1
40 42 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 4 1 1.220000e+02 4.000000e+02
1.220000e+02 4.000000e+02
2 1 15 1 1.200000e+02 4.000000e+02
1.200000e+02 4.000000e+02
4 1 15 1 1.180000e+02 4.000000e+02
1.180000e+02 4.000000e+02
1 2 3 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
1 2 16 1 1.240000e+02 4.000000e+02
1.240000e+02 4.000000e+02
3 2 16 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
2 3 6 1 1.220000e+02 4.000000e+02
1.220000e+02 4.000000e+02
2 3 25 1 1.180000e+02 4.000000e+02
1.180000e+02 4.000000e+02
6 3 25 1 1.200000e+02 4.000000e+02
1.200000e+02 4.000000e+02
1 4 5 1 1.210000e+02 4.000000e+02
1.210000e+02 4.000000e+02
1 4 26 1 1.200000e+02 4.000000e+02
1.200000e+02 4.000000e+02
5 4 26 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
4 5 6 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
4 5 10 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
6 5 10 1 1.220000e+02 4.000000e+02
1.220000e+02 4.000000e+02
3 6 5 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
3 6 7 1 1.210000e+02 4.000000e+02
1.210000e+02 4.000000e+02
5 6 7 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
6 7 8 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
6 7 17 1 1.210000e+02 4.000000e+02
1.210000e+02 4.000000e+02
8 7 17 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
7 8 9 1 1.250000e+02 4.000000e+02
1.250000e+02 4.000000e+02
7 8 27 1 1.160000e+02 4.000000e+02
1.160000e+02 4.000000e+02
9 8 27 1 1.180000e+02 4.000000e+02
1.180000e+02 4.000000e+02
8 9 10 1 1.200000e+02 4.000000e+02
1.200000e+02 4.000000e+02
8 9 12 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
10 9 12 1 1.240000e+02 4.000000e+02
1.240000e+02 4.000000e+02
5 10 9 1 1.150000e+02 4.000000e+02
1.150000e+02 4.000000e+02
5 10 11 1 1.220000e+02 4.000000e+02
1.220000e+02 4.000000e+02
9 10 11 1 1.240000e+02 4.000000e+02
1.240000e+02 4.000000e+02
9 12 13 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
9 12 14 1 1.220000e+02 4.000000e+02
1.220000e+02 4.000000e+02
13 12 14 1 1.220000e+02 4.000000e+02
1.220000e+02 4.000000e+02
12 13 28 1 1.110000e+02 4.000000e+03
1.110000e+02 4.000000e+02
2 16 20 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
2 16 24 1 1.200000e+02 4.000000e+02
1.200000e+02 4.000000e+02
20 16 24 1 1.120000e+02 4.000000e+02
1.120000e+02 4.000000e+02
7 17 18 1 1.200000e+02 4.000000e+02
1.200000e+02 4.000000e+02
7 17 19 1 1.210000e+02 4.000000e+02
1.210000e+02 4.000000e+02
7 17 29 1 1.130000e+02 4.000000e+02
1.130000e+02 4.000000e+02
18 17 19 1 5.990000e+01 4.000000e+02
5.990000e+01 4.000000e+02
18 17 29 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
19 17 29 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
17 18 19 1 6.010000e+01 4.000000e+02
6.010000e+01 4.000000e+02
17 18 30 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
17 18 31 1 1.180000e+02 4.000000e+02
1.180000e+02 4.000000e+02
19 18 30 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
19 18 31 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
30 18 31 1 1.140000e+02 4.000000e+02
1.140000e+02 4.000000e+02
17 19 18 1 6.000000e+01 4.000000e+02
6.000000e+01 4.000000e+02
17 19 32 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
17 19 33 1 1.180000e+02 4.000000e+02
1.180000e+02 4.000000e+02
18 19 32 1 1.170000e+02 4.000000e+02
1.170000e+02 4.000000e+02
18 19 33 1 1.190000e+02 4.000000e+02
1.190000e+02 4.000000e+02
32 19 33 1 1.150000e+02 4.000000e+02
1.150000e+02 4.000000e+02
16 20 21 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
16 20 34 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
16 20 35 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
21 20 34 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
21 20 35 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
34 20 35 1 1.070000e+02 4.000000e+02
1.070000e+02 4.000000e+02
20 21 22 1 1.130000e+02 4.000000e+02
1.130000e+02 4.000000e+02
20 21 36 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
20 21 37 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
22 21 36 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
22 21 37 1 1.080000e+02 4.000000e+02
1.080000e+02 4.000000e+02
36 21 37 1 1.080000e+02 4.000000e+02
1.080000e+02 4.000000e+02
21 22 23 1 1.120000e+02 4.000000e+02
1.120000e+02 4.000000e+02
21 22 38 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
23 22 38 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
22 23 24 1 1.140000e+02 4.000000e+02
1.140000e+02 4.000000e+02
22 23 39 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
22 23 40 1 1.080000e+02 4.000000e+02
1.080000e+02 4.000000e+02
24 23 39 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
24 23 40 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
39 23 40 1 1.080000e+02 4.000000e+02
1.080000e+02 4.000000e+02
16 24 23 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
16 24 41 1 1.090000e+02 4.000000e+02
1.090000e+02 4.000000e+02
16 24 42 1 1.120000e+02 4.000000e+02
1.120000e+02 4.000000e+02
23 24 41 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
23 24 42 1 1.100000e+02 4.000000e+02
1.100000e+02 4.000000e+02
41 24 42 1 1.080000e+02 4.000000e+02
1.080000e+02 4.000000e+02
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
4 1 2 3 1 1.830000e+02 5.000000e+00
3.000000e+00 1.830000e+02 5.000000e+00 3.000000e+00
2 1 4 5 1 1.740000e+02 5.000000e+00
3.000000e+00 1.740000e+02 5.000000e+00 3.000000e+00
1 2 3 6 1 1.820000e+02 5.000000e+00
3.000000e+00 1.820000e+02 5.000000e+00 3.000000e+00
1 2 16 20 1 1.860000e+02 5.000000e+00
3.000000e+00 1.860000e+02 5.000000e+00 3.000000e+00
2 3 6 5 1 1.730000e+02 5.000000e+00
3.000000e+00 1.730000e+02 5.000000e+00 3.000000e+00
1 4 5 6 1 1.810000e+02 5.000000e+00
3.000000e+00 1.810000e+02 5.000000e+00 3.000000e+00
4 5 6 3 1 1.840000e+02 5.000000e+00
3.000000e+00 1.840000e+02 5.000000e+00 3.000000e+00
4 5 10 9 1 3.480000e+02 5.000000e+00
3.000000e+00 3.480000e+02 5.000000e+00 3.000000e+00
3 6 7 8 1 9.000000e+00 5.000000e+00
3.000000e+00 9.000000e+00 5.000000e+00 3.000000e+00
6 7 8 9 1 1.670000e+02 5.000000e+00
3.000000e+00 1.670000e+02 5.000000e+00 3.000000e+00
6 7 17 18 1 2.580000e+02 5.000000e+00
3.000000e+00 2.580000e+02 5.000000e+00 3.000000e+00
7 8 9 10 1 1.850000e+02 5.000000e+00
3.000000e+00 1.850000e+02 5.000000e+00 3.000000e+00
8 9 10 5 1 1.840000e+02 5.000000e+00
3.000000e+00 1.840000e+02 5.000000e+00 3.000000e+00
8 9 12 13 1 3.570000e+02 5.000000e+00
3.000000e+00 3.570000e+02 5.000000e+00 3.000000e+00
9 12 13 28 1 1.810000e+02 5.000000e+00
3.000000e+00 1.810000e+02 5.000000e+00 3.000000e+00
2 16 20 21 1 7.200000e+01 5.000000e+00
3.000000e+00 7.200000e+01 5.000000e+00 3.000000e+00
2 16 24 23 1 2.940000e+02 5.000000e+00
3.000000e+00 2.940000e+02 5.000000e+00 3.000000e+00
7 17 18 19 1 2.100000e+02 5.000000e+00
3.000000e+00 2.100000e+02 5.000000e+00 3.000000e+00
7 17 19 18 1 1.470000e+02 5.000000e+00
3.000000e+00 1.470000e+02 5.000000e+00 3.000000e+00
17 18 19 32 1 1.410000e+02 5.000000e+00
3.000000e+00 1.410000e+02 5.000000e+00 3.000000e+00
16 20 21 22 1 1.800000e+01 5.000000e+00
3.000000e+00 1.800000e+01 5.000000e+00 3.000000e+00
20 21 22 23 1 3.330000e+02 5.000000e+00
3.000000e+00 3.330000e+02 5.000000e+00 3.000000e+00
21 22 23 24 1 2.500000e+01 5.000000e+00
3.000000e+00 2.500000e+01 5.000000e+00 3.000000e+00
22 23 24 16 1 3.420000e+02 5.000000e+00
3.000000e+00 3.420000e+02 5.000000e+00 3.000000e+00
>
> -- original message --
>
> Hi all,
>
> I am trying to simulate a small organic molecule (42 atoms with 18
> hydrogens among them) in water (SPCE). The force field was generated
> with X2TOP utility using GROMOS96 force field. All bonds, pairs,
> angles, dihedrals, etc are OK and the system runs OK but sometimes it
> craches producing several PDB files and CORE files. The message in the
> standart output is:
>
> t = 122.523 ps: Water molecule starting at atom 2497 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Warning: 1-4 interaction between 62 and 80 at distance
> 2653175545629928960.000 which is larger than the 1-4 table size 2.450
> 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
>
> t = 122.524 ps: Water molecule starting at atom 1009 can not be settled.
> Check for bad contacts and/or reduce the timestep.
>
> t = 122.524 ps: Water molecule starting at atom 1693 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> The timestep is 1fs, the temperature varies from 25C up to 70C,
> barostat is turned on. If I reduce the timestep to 0.25fs, the problem
> does not appear fortunately but I would like to keep it equal to 1fs.
> I am sure the problem is with an organic molecule because it doesn't
> appear with SPCE water only. In the organic molecule nexcl=3 and all
> angles are defined well. Trying LINCS instead, I got a big number of
> warnings (>1000).
>
> What can be wrong with my force field (generated by X2TOP) else ?
>
> Thanks in advance.
>
>
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