[gmx-users] Problem running equilibration step

Felipe Merino felipe.merino at mpi-dortmund.mpg.de
Thu Jul 16 12:45:06 CEST 2015


The error is rather clear. There are atoms that are not coupled to any 
thermostat. In principle, you can set tc-grps to System and only give 
one tau and reference temperature and it will work. If you need a more 
elaborated scheme, them you can supply group definitions (if not 
available but default) with an index file.


On 16/07/15 12:37, Priyanka Patel wrote:
> Dear all,
> I am doing simulation of DNA nano-structure using Gromacs (VERSION 4.6.5)
> by applying CHARMM26 force field and TIP4P water model. The energy
> minimization step is working fine but i am facing problem during
> equilibration step due to wrong *nvt.mdp* file.
> Can you please guide me, which kind of parameter should be change in
> *nvt.mdp* file for DNA nano-structure MD simulation. I am following Justin
> A. Lemkul's tutorial (Lysozyme in water) using following link;
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> I am getting error like this;
> Fatal error:
> 318 atoms are not part of any of the T-Coupling groups
> My command line is like this;
> *grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr *
> I am also attaching the modified nvt.mdp file according to DNA MD
> simulation requirement for your reference.
> I am working under the government organization, National center for Cell
> Science meant for non-profit research. I shall be highly obliged if you
> could help me to solve this problem.

Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306

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