Calculus of the energy of interaction bweteen chains

User discussions
1

GROMACS version: 2019.2
GROMACS modification: No
I want to calculate the energy of interaction between chain A and C of my protein, to this I introduce both proteins in my ndx file, when I run the md simulation i get the following error

Program: gmx grompp, version 2019.2
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2667)

Fatal error:
Atom 1 in multiple T-Coupling groups (1 and 2)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I did the index using gmx make_index

what can I do?

2

Please post your .mdp file and the commands used to produce any custom groups.

3

hi

the coomand line is
gmx grompp -f …/MDP/md.mdp -n …/0_topol/protein.ndx -c …/3_npt/prot_npt_10.gro -t …/3_npt/prot_npt_10.cpt -p …/0_topol/topol.top -o prot_md_01.tpr

and the md.mdp and the index files are attached belowmd.mdp (2.3 KB)

the index was done using the following commands

#create gromacs index
gmx make_ndx -f protein.pdb -o protein.ndx << EOF
1 & chain A
1 & chain C
name 10 Protein_chain_A
name 11 Protein_chain_C
q
EOF