[gmx-users] protein-ligand complex fatal error

[Justin Lemkul]

On 12/12/14 9:19 AM, Yaser Hosseini wrote:
> hi
>
> i just want to run
>
> mdrun -v deffnm nvt
>
> i run every command in this tutorials
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html
>   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
>

Be careful in trying to use exactly what the tutorial does with other systems; 
specifically, if you're using a different force field, you shouldn't be using 
the tutorial's .mdp files.

> 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 .
>

The list does not accept attachments.  If you want to share files, please upload 
them to a file-sharing server and provide the relevant URL(s).  Include .mdp 
files.  A full description of what you have done thus far, as well as the output 
of energy minimization, is needed.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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