[gmx-users] Bond length not finite error

gromacs query gromacsquery at gmail.com
Fri Mar 14 02:19:38 CET 2014

Hi All

I am simulating charmm36 popc membrane with ions and got this error (NPT
with position restraints) before this I did minimization and NVT with

I could not find "Bond length not finite" error in archive.

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
    8.18304e+03    4.74407e+04    3.42709e+04    3.20853e+02    5.14831e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.
   -6.86739e+04    4.59295e+03   -2.98874e+05   -2.76148e+04    9.43012e-01
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -2.95205e+05    1.01717e+05   -1.93487e+05    3.01097e+02    1.06138e+03
   Constr. rmsd

DD  step 9 load imb.: force 55.3%

At step 10 the performance loss due to force load imbalance is 23.9 %

NOTE: Turning on dynamic load balancing

Program mdrun, VERSION 4.6.3
Source code file:
/sbcb/packages/src/gromacs/gromacs-4.6.3/src/mdlib/clincs.c, line: 1404

Fatal error:
Bond length not finite.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


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