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

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 2 11:46:41 CEST 2008

Chitrita Duttaroy wrote:
> Hi,
> I am a beginner of Gromacs 3.3.3. <http://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.

I'm guessing those two atoms are the 2 NA+ (most likely).  Every element of your 
system should be included in a T-coupling group.  Your .mdp file probably has 
not assigned the NA+ anywhere (merge it with the solvent in a special group: 


> Thanking you,
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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