> > 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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
