[gmx-users] simulation error
Mario Andres Rodriguez Pineda
mandres at iq.usp.br
Tue Sep 18 06:42:53 CEST 2018
These were the errors until the moment of executing the minimization:
After adding ions grompp:
NOTE 1 [file topol.top, line 37566]:
System has non-zero total charge: -18.999999
Total charge should normally be an integer. See
for discussion on how close it should be to an integer.
step 16: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
tMPI error: Receive buffer size too small for transmission (in valid comm)
Abort (core dumped)
In attach send you the mdp archive for minimization run.
Thanks for your help
Em seg, 17 de set de 2018 às 19:56, Justin Lemkul <jalemkul at vt.edu>
> On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote:
> > Hi everyone.
> > I'm trying simulate a protein in water followin lysozyme tutorial using
> > gromacs 2016.3. When triying minimize the system after make the box and
> > insert a salt concentration the minimization has been stoped sendingme
> > following error:
> > step 16: One or more water molecules can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > Wrote pdb files with previous and current coordinates
> > tMPI error: Receive buffer size too small for transmission (in valid
> > Abort (core dumped)
> Water SETTLE problems are not unusual in energy minimization and are
> often resolved. If, however, such a message immediately precedes a
> failure, then you have a serious problem with either the coordinates or
> topology. mdrun prints out which atom is experiencing the maximum force,
> so start by looking there, as well as reviewing your notes about what
> warnings pdb2gmx or grompp may have issued (but surely you wouldn't have
> ignored any, right? :).
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*
*UNAL- MEDELLÍN *
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