[gmx-users] Bond length not finite error

[Justin Lemkul]

On 3/13/14, 9:19 PM, gromacs query wrote:
> 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
> posres.
>
> 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
>      3.48558e-06
>
> 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
> -------------------------------------------------------
>

Well that's a new one.

The meaning is fairly clear, though.  You have a bond that is infinitely long as 
a result of some nasty unphysical thing happening.  LINCS can't fix the length 
of something infinite, so it fails.  Check your .log file and/or stderr/stdout 
for other useful information.  General advice is at 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.  More than likely, 
your initial equilibration was insufficient or your current run settings are 
leading to instability.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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