[gmx-users] Problem running equilibration step

Priyanka Patel priyanka.patel826 at gmail.com
Thu Jul 16 12:37:36 CEST 2015

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;


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.

Priyanka Patel

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