[gmx-users] protein-ligand complex fatal error

Yaser Hosseini yaser.hosseini.biologist at gmail.com
Fri Dec 12 15:19:16 CET 2014


i just want to run

mdrun -v deffnm nvt

i run every command in this tutorials

 but at the end i got two errors :

There are: 247500 Atoms
Charge group distribution at step 0: 20986 20508 20732 20838
Grid: 7 x 20 x 20 cells

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 300.014 K

Started mdrun on node 0 Tue Dec  9 18:34:03 2014

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    3.82672e+03    4.61912e+03    1.17647e+03    2.38416e+03    6.14760e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    5.52391e+05   -1.62520e+04   -4.11231e+06   -3.79310e+05    1.63515e+00
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
   -3.88200e+06    6.17756e+05   -3.26424e+06   -3.26424e+06    3.00269e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -2.16174e+02   -4.15136e+03    1.57324e-05

DD  step 4 load imb.: force  3.5%

Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/clincs.c, line: 1404

Fatal error:
Bond length not finite.

and this :

> Fatal error:
> 4 particles communicated to PME node 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.

if you want more information i can attach topol.top and em and nvt.log files .

thank you.

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