[gmx-users] Re: simulation crash with GROMOS96 force field
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sun Jan 24 19:17:39 CET 2010
>> 1. Is your system is properly minimized
>
> Of course, it is, based on the energy values.
Don't be so sure! Although since your 0.25 fs timestep --> 1 fs
timestep transition crashes you are likely correct here.
>> **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.
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
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.
Also, Why do you have 4 terms for the bonds?
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1 1.400000e-01 4.000000e+05 1.400000e-01
> 4.000000e+05
Surely you should heave:
; ai aj funct b0 kb
and I'm not sure what happens to those other c2/c3.
Quoting "Vitaly V. Chaban" <vvchaban at 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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