[gmx-users] Problems in energygrps and tc-grps

[Mark Abraham]

Huey Ling Tan wrote:
> Dear gromacs users,
> 
>    I am simulating 2 identical peptide chains in a simulation box with 
> water as solvent. To find the the equilibration, I wanted to calculate 
> the energy of the peptide chains, separately, and then compare between 
> them. 
> 
>    To do that, I changed the energygrps and tc-grps in my .mdp file to 
> peptide_1, peptide_2 and SOL. But I got an error which stated :
>   
>    14892 atoms are not part of any of the T-Coupling groups
> 
>    In fact, I have include all the atoms in my .gro file with these 3 
> groups (peptide_1, peptide_2 and SOL).
> 
>    I appreciate any suggestion and advise. Thanks.

The contents of your index file determine group membership. See section 
8.1 of the manual.

Mark