[gmx-users] program crashes when -table option used

[Yang Ye]

reduce timestep or further minimization/equilibration?

Yang Ye

Dongsheng Zhang wrote:
> Dear GMX users,
>
>
> I have a coarse-grained model whose nonbonded potentials are tabulated,
> so I have to use user defined potential in gromacs. With Yang Ye's great
> help, I can implement the new force field. However, the program always
> crashed because of Large VCM(group rest). I have done a test by run the
> program in two different ways. My new force field uses gromos FF format,
> so I used c6 and c12 parameters.
>
>
> First I ran the program in a normal way, which means I use LJ for
> regular VDWs and 1-4 interactions. The program ran fine.
>
> Second I copied table6-12.xvg to my working directory and rename it to a
> proper name, then I used this table as my user-defined potential for
> VDWs and 1-4 interactions. 
>
> I expect the above two ways give me very similar results. This is true
> for the first 51 steps. In step 52, the second run suddenly crashed
> because of Large VCM(group rest).
>
> The details are as following:
>
> The differences in two mdp files:
>
> 59c59
> < vdw-type                 = user  ;cut-off
> ---
>   
>> vdw-type                 = cut-off;  user  ;cut-off
>>     
>
> The information from two log files:
>
> full2.log (first run):
>
>            Step           Time         Lambda
>              51        0.10200        0.00000
>
>    Energies (kJ/mol)
>            Bond          Angle          LJ-14     Coulomb-14        LJ
> (SR)
>     3.02207e+02    3.00007e+02   -3.73112e+01    0.00000e+00   -2.27638e
> +02
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy
> Temperature
>     0.00000e+00    3.37264e+02    1.01670e+03    1.35397e+03    3.09963e
> +02
>  Pressure (bar)
>     4.78614e+00
>
>            Step           Time         Lambda
>              52        0.10400        0.00000
>
>    Energies (kJ/mol)
>            Bond          Angle          LJ-14     Coulomb-14        LJ
> (SR)
>     3.00485e+02    2.99534e+02   -3.73372e+01    0.00000e+00   -2.27861e
> +02
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy
> Temperature
>     0.00000e+00    3.34820e+02    1.01849e+03    1.35331e+03    3.10508e
> +02
>  Pressure (bar)
>     4.73457e+00
>
>            Step           Time         Lambda
>              53        0.10600        0.00000
>
>    Energies (kJ/mol)
>            Bond          Angle          LJ-14     Coulomb-14        LJ
> (SR)
>     2.98871e+02    2.99071e+02   -3.73627e+01    0.00000e+00   -2.28077e
> +02
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy
> Temperature
>     0.00000e+00    3.32503e+02    1.02011e+03    1.35262e+03    3.11004e
> +02
>  Pressure (bar)
>     4.67219e+00
>
>
>
>
> full.log (second run):
>
>            Step           Time         Lambda
>              51        0.10200        0.00000
>
>    Energies (kJ/mol)
>            Bond          Angle          LJ-14     Coulomb-14        LJ
> (SR)
>     3.02206e+02    3.00007e+02   -3.73112e+01    0.00000e+00   -2.27636e
> +02
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy
> Temperature
>     0.00000e+00    3.37266e+02    1.01670e+03    1.35397e+03    3.09963e
> +02
>  Pressure (bar)
>     4.78604e+00
>
>            Step           Time         Lambda
>              52        0.10400        0.00000
>
> Large VCM(group rest): -362781422043267072.00000,
> 46998104838242304.00000, -95810352322707456.00000, ekin-cm:          inf
>    Energies (kJ/mol)
>            Bond          Angle          LJ-14     Coulomb-14        LJ
> (SR)
>     3.00484e+02    2.99534e+02   -9.09769e+31    0.00000e+00   -2.27860e
> +02
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy
> Temperature
>     0.00000e+00   -9.09769e+31            inf            inf
> inf
>  Pressure (bar)
>             inf
>
>            Step           Time         Lambda
>              53        0.10600        0.00000
>
>
> Compare step 51 in two cases, every item has very similar value. In step
> 52, the second run give me very large value of LJ14. This causes the
> problem. However I compare the output xtc files at step 52 i those twp
> runs. They are identical. It really surprises me that LJ-14 is so large
> in the second run.
>
>
> Any suggest to find what's wrong will be highly appreciated. If you need
> more information, please let me know.
>
> All the best!
>
> Dongsheng
>
>
>
>
>
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