[gmx-users] simulation error

Justin Lemkul jalemkul at vt.edu
Tue Sep 18 00:55:46 CEST 2018

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 the
> 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 comm)
> 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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