# Temperature coupling **URL:** \ **Category:** User discussions\ **Created:** [June 23, 2026, 1:05pm UTC](https://gromacs.bioexcel.eu/t/temperature-coupling/13547 "2026-06-23T13:05:47Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![slaa1999](https://avatars.discourse-cdn.com/v4/letter/s/a9a28c/32.png) [@slaa1999](https://gromacs.bioexcel.eu/u/slaa1999)\ **Post date:** [June 23, 2026, 1:05pm UTC](https://gromacs.bioexcel.eu/t/temperature-coupling/13547/1 "2026-06-23T13:05:47Z")
GROMACS version:2020.7 GROMACS modification: Yes/No Hello All, Excuse my novice experience in GROMACS MD simulation. What is the approach in setting up proper control of temperature coupling. I have system with a metalloprotein(Zinc Ions) and DNA scaffold. My logic in approaching this situation is as follows I will create an index file, creating the below naming scheme. in .mpd files, tc-grps = SOLUTE SOLVENT SOLUTE = will consist of protein, DNA, Zinc ions and also counterions(NA+) SOLVENT = water artoms Is this correct ?, or this flawed. Also should I define the bulk counterions as their own thermostat group? Below are the components of system(Cysteine amino residues have their own RES ID, so i believe standard tc-grps = PROTEIN NON-PROTEIN will not work for my system) Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 130 Protein residues There are: 20 Other residues There are: 38 DNA residues There are: 28 Ion residues There are: 11632 Water residues Analysing Protein… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… 0 System : 38348 atoms 1 Protein : 2052 atoms 2 Protein-H : 1014 atoms 3 C-alpha : 130 atoms 4 Backbone : 390 atoms 5 MainChain : 522 atoms 6 MainChain+Cb : 638 atoms 7 MainChain+H : 654 atoms 8 SideChain : 1398 atoms 9 SideChain-H : 492 atoms 10 Prot-Masses : 2052 atoms 11 non-Protein : 36296 atoms 12 Other : 164 atoms 13 CY1 : 10 atoms 14 CY2 : 10 atoms 15 CY3 : 10 atoms 16 CY4 : 10 atoms 17 CY5 : 10 atoms 18 CY6 : 10 atoms 19 CY7 : 10 atoms 20 CY8 : 10 atoms 21 ZN1 : 1 atoms 22 ZN2 : 1 atoms 23 CY9 : 10 atoms 24 1CY : 10 atoms 25 2CY : 10 atoms 26 3CY : 10 atoms 27 4CY : 10 atoms 28 5CY : 10 atoms 29 6CY : 10 atoms 30 7CY : 10 atoms 31 ZN3 : 1 atoms 32 ZN4 : 1 atoms 33 Na+ : 28 atoms 34 DNA : 1208 atoms 35 CY1 : 10 atoms 36 CY2 : 10 atoms 37 CY3 : 10 atoms 38 CY4 : 10 atoms 39 CY5 : 10 atoms 40 CY6 : 10 atoms 41 CY7 : 10 atoms 42 CY8 : 10 atoms 43 ZN1 : 1 atoms 44 ZN2 : 1 atoms 45 CY9 : 10 atoms 46 1CY : 10 atoms 47 2CY : 10 atoms 48 3CY : 10 atoms 49 4CY : 10 atoms 50 5CY : 10 atoms 51 6CY : 10 atoms 52 7CY : 10 atoms 53 ZN3 : 1 atoms 54 ZN4 : 1 atoms 55 Na+ : 28 atoms 56 Ion : 28 atoms 57 CY1 : 10 atoms 58 CY2 : 10 atoms 59 CY3 : 10 atoms 60 CY4 : 10 atoms 61 CY5 : 10 atoms 62 CY6 : 10 atoms 63 CY7 : 10 atoms 64 CY8 : 10 atoms 65 ZN1 : 1 atoms 66 ZN2 : 1 atoms 67 CY9 : 10 atoms 68 1CY : 10 atoms 69 2CY : 10 atoms 70 3CY : 10 atoms 71 4CY : 10 atoms 72 5CY : 10 atoms 73 6CY : 10 atoms 74 7CY : 10 atoms 75 ZN3 : 1 atoms 76 ZN4 : 1 atoms 77 Na+ : 28 atoms 78 Water : 34896 atoms 79 SOL : 34896 atoms 80 non-Water : 3452 atoms 81 Water\_and\_ions : 34924 atoms Any suggestions or tips would be greatly appreciated. Thanks ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 23, 2026, 1:20pm UTC](https://gromacs.bioexcel.eu/t/temperature-coupling/13547/2 "2026-06-23T13:20:42Z")
Nowadays there are extremely few systems that require multiple temperature coupling groups. I would suggest to use a single group. ---
**Author:** ![slaa1999](https://avatars.discourse-cdn.com/v4/letter/s/a9a28c/32.png) [@slaa1999](https://gromacs.bioexcel.eu/u/slaa1999)\ **Post date:** [June 24, 2026, 2:11pm UTC](https://gromacs.bioexcel.eu/t/temperature-coupling/13547/3 "2026-06-24T14:11:02Z")
Okay, thanks for the reply. Wow, you are right. I done short experimentation: exp\_1 ::( tc\_grps = **non\_water** (protein+DNA+Zn+NA(counterions) : **Water** atoms exp\_2 ::( tc\_grps = **Solute** (protein+DNA+Zn): **Solvent** (Water and NA) exp\_3 :: (tc-grps - **System** (whole system) Ran a MD simulation on each experimentation, it seems to be case oddly enough the experiment 3 produced the most stable MD analysis(RMSD calculations of the trajectory analysis of the protein). Is it fine Hess, to use the whole system for my tc-grps for my .mdp file. I am actually suprised this worked out the way it did, I was expecting a different result. because on this page : [GROMACS MDP File Parameters: integrator, thermostat, barostat, and cutoffs explained - Compchems](https://www.compchems.com/gromacs-mdp-file-parameters/#mdp-file-for-nvt-equilibrations) states that " You can create separate groups for the thermostat with the `tc-groups` parameter. It is generally recommendable to create at least two groups, consisting of the protein (`Protein`) and the rest of the system (`Non-protein`)." ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 24, 2026, 4:27pm UTC](https://gromacs.bioexcel.eu/t/temperature-coupling/13547/4 "2026-06-24T16:27:17Z")
Very likely your results are just the statistical variation between simulations. I would not expect any measurable difference between those settings. The advice for separate T-coupling groups is relevant for GROMACS versions of 15 years ago.