[gmx-users] Re: simulation crash with GROMOS96 force field
Vitaly V. Chaban
vvchaban at gmail.com
Sun Jan 24 19:36:30 CET 2010
>
> 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" <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.
More information about the gromacs.org_gmx-users
mailing list