Dear Vitaly:
Justin raises the point well, so that should be addressed first. If,
however, you still have problems then there's the only thing that I
can think of:
1. put a single solute in a large vacuum box and use the sd
integrator. Can you reproduce the problem?
2. Remove the dihedral parameters entirely. Can you reproduce the problem?
3. Remove also the angle parameters entirely. Can you reproduce the problem?
This may help you to track down where the problem is. I have no
experience with x2top so this is probably where I will leave off.
Chris.
Quoting "Vitaly V. Chaban" <vvcha...@gmail.com>:
There's your problem (although in a different manner than I thought).
If you have, for example, 3 solutes, then you should have
[ molecules ]
CIP 3
-NOT-
[ molecules ]
CIP 1
Of course, the number of moleules in .top and .gro files coincides.
Otherwise, one would have had immediate crash.
CIP 3 -> [ moleculetype ] !
Although probably we're miscommunicating on this as I can't see how
that could be stable for 500 ps...
As an aside, can you really put cgnr in non-ascending order? I have no
reason to think that you can not, but since I've never seen it before
it's worth checking.
I checked already. It is not a reason. Even if one treats all the
molecule as the only charge group, the crash appears.
Also, Why do you have 4 terms for the bonds?
..................
and I'm not sure what happens to those other c2/c3.
I do not know also. :) This is just what was generated by X2TOP. I
tried to use only one constant instead but it didn't solve the
problem.
Quoting "Vitaly V. Chaban" <vvcha...@gmail.com>:
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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