[gmx-users] mdrun error

[Justin A. Lemkul]

Since alamethicin works on its own, it suggests to me that the introduction of
alamethicin into POPC is what's causing the problem, and judging by the
enormous potential energies and forces, it appears to be bad contacts/atomic
overlap (at least, that's been the cause of problems in my experience).  How
are you generating your starting structure?

-Justin

>
> Thanks for your help. I figured the problem out but am getting an error
> again. I have alamethicin in popc and water. Since alamethicin has some non
> standard residue i made topology file in text editor and ran mdrun with only
> alamethicin. It went fine. But when i am tring to minimize alamethicin in
> popc mdrum probably does not recognize the starting of second chain and gives
> me following error:
>
> Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is
> larger than the 1-4 table size 1.000 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
> Step=    1, Dmax= 1.0e-02 nm, Epot=  3.25524e+09 Fmax= 1.00321e+09, atom=
> 2441
> Step=    2, Dmax= 1.2e-02 nm, Epot=  2.21743e+09 Fmax= 1.82388e+08, atom=
> 12852
> Step=    3, Dmax= 1.4e-02 nm, Epot=  1.95672e+09 Fmax= 7.44135e+07, atom= 262
> Step=    4, Dmax= 1.7e-02 nm, Epot=  1.88109e+09 Fmax= 4.32188e+07, atom= 260
> Step=    5, Dmax= 2.1e-02 nm, Epot=  1.84989e+09 Fmax= 2.77292e+07, atom= 262
> Step=    6, Dmax= 2.5e-02 nm, Epot=  1.83083e+09 Fmax= 1.89783e+07, atom= 258
> Step=    7, Dmax= 3.0e-02 nm, Epot=  1.81606e+09 Fmax= 9.97167e+06, atom= 253
> Step=    8, Dmax= 3.6e-02 nm, Epot=  1.79660e+09 Fmax= 2.09557e+07, atom= 258
> Step=    9, Dmax= 4.3e-02 nm, Epot=  1.78793e+09 Fmax= 1.63547e+07, atom= 259
> Step=   10, Dmax= 5.2e-02 nm, Epot=  1.77532e+09 Fmax= 7.54157e+06, atom=
> 12539
> Step=   11, Dmax= 6.2e-02 nm, Epot=  1.74488e+09 Fmax= 7.42417e+06, atom=
> 12539
> Step=   12, Dmax= 7.4e-02 nm, Epot=  1.70998e+09 Fmax= 7.28331e+06, atom=
> 12539
> Step=   13, Dmax= 8.9e-02 nm, Epot=  1.66920e+09 Fmax= 7.11508e+06, atom=
> 12539
> Wrote pdb files with previous and current coordinates
>
> Back Off! I just backed up step13.pdb to ./#step13.pdb.1#
>
> Back Off! I just backed up step14.pdb to ./#step14.pdb.1#
> Wrote pdb files with previous and current coordinates
>
> my pdb file at 164 to 169 is:
> ATOM    164  CZ  PHL    21      44.000  52.840  35.170  1.00  0.00
> ATOM    165  HZ  PHL    21      44.990  53.260  35.090  1.00  0.00
> ATOM    166  CX  PHL    21      38.140  50.450  37.160  1.00  0.00
> ATOM    167  OY  PHL    21      37.940  49.350  38.060  1.00  0.00
> ATOM    168  HY  PHL    21      37.040  48.940  37.950  1.00  0.00
> ATOM    169  CA  ACE    22      53.840  44.410  66.930  1.00  0.00
>
> I think it is not recognising different chain. Am i right? Please help me.
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=========================================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

=========================================================