[gmx-users] Re: simulation crash with GROMOS96 force field
Justin A. Lemkul
jalemkul at vt.edu
Sun Jan 24 19:39:54 CET 2010
Vitaly V. Chaban wrote:
>> 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 ] !
>
[molecules] is a different directive than [moleculetype]. Under [moleculetype]
you find the name of the molecule and the number of exclusions, not the number
of molecules. Do you have only one solute? If so, then it cannot be the first
molecule in the system, given the atom numbers in the crash you reported before.
Is everything in the [molecules] directive in the same order as your
coordinate file? Did grompp give any atom type mismatch warnings?
-Justin
>
>
>
>> 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" <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.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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