# Should I use two T-coupling groups for ice+graphene? **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [December 20, 2024, 5:40am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863 "2024-12-20T05:40:55Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![wudiazhu](https://avatars.discourse-cdn.com/v4/letter/w/5f8ce5/32.png) [@wudiazhu](https://gromacs.bioexcel.eu/u/wudiazhu)\ **Post date:** [December 20, 2024, 5:40am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/1 "2024-12-20T05:40:55Z")
GROMACS version: 2023 Hi everyone. I was running the growth of ice on a substrate surface (graphene). I found it so different between using two T-coupling groups and using one T-couping group. When I set the substrate and ice as two independent T-coupling groups, the bottom layer of ice (the layer in contact with substrate) is hard to maintain its original crystal, or to say the bottom layer of ice melts quickly. > Tcoupl = V-rescale > tau\_t = 0.2 0.2 > tc\_grps = SOL non-water > ref\_t = 180 180 When I put the whole system into one T-couping group, the ice crystal was well maintained. > Tcoupl = V-rescale > tau\_t = 0.2 > tc\_grps = system > ref\_t = 180 The substrate is set to be frozen in these two cases > freezegrps = non-water > freezedim = Y Y Y I want the bottom layer of ice to maintain its crystal structure, but I am not sure which one is correct? And what makes it so diffenet when seperate it into two T-coupling groups? Thank you so much! I will really appreciate it if you can do me this favor! ---
**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:** [December 20, 2024, 8:03am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/2 "2024-12-20T08:03:52Z")
I would think that there should be no difference between the two considering that all atoms in graphene are frozen. Can you report here what mdrun reports for nrdf for the two groups and the single group in the md.log files? Note that a tau\_t of 0.2 is very short. Likely this doesn’t lead to any issues, but I would suggest to use tau\_t=1 ---
**Author:** ![wudiazhu](https://avatars.discourse-cdn.com/v4/letter/w/5f8ce5/32.png) [@wudiazhu](https://gromacs.bioexcel.eu/u/wudiazhu)\ **Post date:** [December 20, 2024, 8:35am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/3 "2024-12-20T08:35:31Z")
Thank you so much for your reply! I don’t quite understand what “nrdf” stands for, but I try to search it in both of the log files. In the two T-coupling groups, it shows: > grpopts: > nrdf: 37821 0 > ref-t: 180 180 > tau-t: 0.2 0.2 In the one T-coupling group, it shows: > grpopts: > nrdf: 19206.8 > ref-t: 180 > tau-t: 0.2 I will show the snapshots of bottom layer ice of these two situations after 50 ns run: ![图片](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a15416f0136eb29a39547ae1c5ede13f6f65b0b4.png) Do we have any creterian for the tau\_t? It is said that the smaller tau\_t, the better temperature control. Isn’t 0.2 better than 1.0? Thank you once again for your reply! ---
**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:** [December 20, 2024, 8:43am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/4 "2024-12-20T08:43:47Z")
nrdf stands for number of degrees of freedom. I would expect the number to be approximately the same, but they clearly are not. I suppose the number of degrees of freedom is too high when using two groups. Are the T-coupling groups really the only thing you changed between the two setups? ---
**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:** [December 20, 2024, 8:49am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/5 "2024-12-20T08:49:50Z")
I reproduced the issue. This is a bug in GROMACS. You can use one t-coupling group for the whole system to avoid this bug. ---
**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:** [December 20, 2024, 8:56am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/6 "2024-12-20T08:56:11Z")
My last answer was incorrect. The seem to be two issues with counting the number of degrees of freedom. One with frozen atoms and constraints and another one with frozen atoms being in the same group as non-frozen atoms. The only way I can get correct counts for my test system is when using two separate T-coupling groups and removing all constraints between frozen atoms. ---
**Author:** ![wudiazhu](https://avatars.discourse-cdn.com/v4/letter/w/5f8ce5/32.png) [@wudiazhu](https://gromacs.bioexcel.eu/u/wudiazhu)\ **Post date:** [December 20, 2024, 9:31am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/7 "2024-12-20T09:31:00Z")
I am sure T-coupling groups really the only difference. Thank you so much! And by the way, are you one of the GROMACS developers? I really appreciate you! ---
**Author:** ![wudiazhu](https://avatars.discourse-cdn.com/v4/letter/w/5f8ce5/32.png) [@wudiazhu](https://gromacs.bioexcel.eu/u/wudiazhu)\ **Post date:** [December 20, 2024, 11:21am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/8 "2024-12-20T11:21:48Z")
I have removed the frozon group and I think I should use two T-coupling groups. I post my result here: ![f4435e09111b46916fa426206e54f5a](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/830b46f4d5a6b64f5bdf1857620fdb8928f28e83.png) No freeze substrate, it seems to be normal. The nrdf 111134 and 37821+73314 are almost the same. When freeze substrate, 19206.8 =! 37821+0. But two T groups one should be right because it is 37821, as the same when no freeze. I think there is something wrong when there are freezon atoms in one T group. ---
**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:** [December 20, 2024, 11:26am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/9 "2024-12-20T11:26:55Z")
Yes. I found the issue and have a fix. The issue appears when fully frozen atoms are in the same T-coupling group as the non-frozen atoms. Using two temperature coupling groups avoids this issue. It seems that constraints do not affect this at all. My previous comment on that was incorrect. ---
**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:** [December 20, 2024, 11:39am UTC](https://gromacs.bioexcel.eu/t/should-i-use-two-t-coupling-groups-for-ice-graphene/10863/10 "2024-12-20T11:39:36Z")
The issue and link to the fix are here: > **[Having fully frozen atoms in the same T-coupling group and non-frozen atoms...](https://gitlab.com/gromacs/gromacs/-/issues/5261)** > > When atoms frozen along all dimensions are present in a temperature coupling group together with non-frozen atoms, the number of degrees of freedom of the temperature coupling group...