[gmx-users] Please help with all-angles constraint ption

Justin Lemkul jalemkul at vt.edu
Fri Jul 20 13:06:37 CEST 2012

On 7/20/12 6:46 AM, radhika jaswal wrote:
> Dear all,
> I did NVT simulations of a number of molecules with double bond. But when i analysed the results i realised that double bond has been converted to single bond and sp2 hybridisation has also changed to sp3. I was doing with all bonds constraint option. But when i started with all angles constraint option it kept on processing on version 3.3.1 and  with many fatal errors on version 4.5.4.

Bonds do not break and form in classical MD, and hybridization cannot change. 
If you are observing distortions in the structure, then likely your topology is 
ill-suited to address the atoms involved.  Correct use of improper dihedrals 
should keep sp2 groups planar.


> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: domdec.c, line: 6436
> Fatal error:
> There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 1.69222 nm
> Change the number of nodes or mdrun option -rcon or your LINCS settings
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------

Not all systems can be divided into any arbitrary number of DD cells.  See here:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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