[gmx-users] Error in T-coupling of 2 atoms in T-couplingGroups

Chitrita Duttaroy rinkduro at gmail.com
Thu Oct 2 10:52:41 CEST 2008


I am a beginner of Gromacs 3.3.3.

I have done position restrined grompp with -f pr.mdp, -r .gro (water box
having charge -2e), -c .gro and -p .top (produced by genbox). The output is
a .tpr file.
Then to neutralize the solution with Na+ ion I used genion by -s .tpr -o
.gro - pname NA+ -np 2 -g .log.
Then in the .top file in [molecule] portion I have changed #mol of SOL by
reducing it by 2 and added NA+ of 2 mol to match the coordinate with .gro.
And also deleted the .tpr file. Upto this step everything was OK.
In next step again position restrained grompp was done using .gro file
containing 2 Na+ ions. But which showed a Fatal error --

Fatal error:
2 atoms are not part of any of the T-coupling groups.

So .tpr file is not generated. I am not understanding what to do now.....
Please help as early as possible.

Thanking you,

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