# Gromacs not reading POSRES even though it is pointed to in topology **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, restraints, simulation-setup\ **Created:** [June 2, 2022, 3:42pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255 "2022-06-02T15:42:54Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![dkonstan](https://avatars.discourse-cdn.com/v4/letter/d/87869e/32.png) [@dkonstan](https://gromacs.bioexcel.eu/u/dkonstan)\ **Post date:** [June 2, 2022, 3:42pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/1 "2022-06-02T15:42:55Z")
GROMACS versions: 2022 and 2021 GROMACS modification: No Hi gromacs, I am running a simulation of a protein with water and some other ingredients and I am having trouble restraining the protein heavy atoms, even though I specify #ifdef POSRES #include “posre\_Protein\_chain\_A2.itp” #endif in the protein topology component itp file and define = -DPOSRES in the mdp file. The posre\_\* file has all the heavy atoms of the protein listed with restraint strengths. Below is my topology for your reference. The Urea.itp and TMAO.itp files are defined elsewhere and included here, as are the other itp files. I can post them too if needed. Thank you very much! Dan * * * ; Include forcefield parameters #include “/gpfs/loomis/project/hammes\_schiffer/as3586/shslocal/apps/gromacs/share/gromacs/top/amber14sb\_OL15.ff/forcefield.itp” [atomtypes] ; name mass charge ptype sigma epsilon CUR 12.0107 0.921 A 0.37700 0.41700 HUR 1.00800 0.285 A 0.15800 0.08800 OUR 15.99940 -0.675 A 0.31000 0.56000 NUR 14.0067 -0.693 A 0.31100 0.50000 OTM 15.99940 -0.910 A 0.32660 0.63790 NTM 14.0067 0.700 A 0.29260 0.83600 CTM 12.01100 -0.260 A 0.36000 0.28260 HTM 1.00800 0.110 A 0.21010 0.07730 [nonbond\_params] ; i j func sigma epsilon (urea-TMAO epsilon scaled by 1.10) CUR CTM 1 0.36840 0.37761 CUR HTM 1 0.28144 0.19749 CUR OTM 1 0.35090 0.56733 CUR NTM 1 0.33213 0.64948 HUR CTM 1 0.23849 0.17347 HUR HTM 1 0.18220 0.09072 HUR OTM 1 0.22716 0.26062 HUR NTM 1 0.21501 0.29836 OUR CTM 1 0.33407 0.43760 OUR HTM 1 0.25521 0.22886 OUR OTM 1 0.31819 0.65745 OUR NTM 1 0.30117 0.75264 NUR CTM 1 0.33460 0.41349 NUR HTM 1 0.25562 0.21626 NUR OTM 1 0.31871 0.62123 NUR NTM 1 0.30166 0.71118 ; i j func sigma epsilon (TMAO-TMAO epsilon scaled by 0.90) OTM OTM 1 0.32660 0.57411 OTM NTM 1 0.30913 0.65724 OTM CTM 1 0.34289 0.38212 OTM HTM 1 0.26195 0.19985 NTM NTM 1 0.29260 0.75240 NTM CTM 1 0.32456 0.43745 NTM HTM 1 0.24794 0.22879 CTM CTM 1 0.36000 0.25434 CTM HTM 1 0.27502 0.13302 HTM HTM 1 0.21010 0.06957 #include “/home/dk758/project/ureaTMAO/NetzM/Urea.itp” #include “/home/dk758/project/ureaTMAO/NetzM/TMAO.itp” ; Include chain topologies #include “topol\_Ion\_chain\_A.itp” #include “topol\_Protein\_chain\_A2.itp” ; Include water topology #include “/gpfs/loomis/project/hammes\_schiffer/as3586/shslocal/apps/gromacs/share/gromacs/top/amber14sb\_OL15.ff/tip3p.itp” #ifdef POSRES\_WATER ; Position restraint for each water oxygen [position\_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include “/gpfs/loomis/project/hammes\_schiffer/as3586/shslocal/apps/gromacs/share/gromacs/top/amber14sb\_OL15.ff/ions.itp” [system] ; Name Built with Packmol [molecules] ; Compound #mols Ion\_chain\_A 1 UR 28 TMO 28 Protein\_chain\_A2 1 SOL 1351 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [June 2, 2022, 4:07pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/2 "2022-06-02T16:07:16Z")
What makes you think the restraints aren’t working? ---
**Author:** ![dkonstan](https://avatars.discourse-cdn.com/v4/letter/d/87869e/32.png) [@dkonstan](https://gromacs.bioexcel.eu/u/dkonstan)\ **Post date:** [June 2, 2022, 4:09pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/3 "2022-06-02T16:09:04Z")
It’s because the heavy atoms move appreciably the traj.trr from the simulation. They clearly are not restrained…they are moving around :-) ---
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [June 2, 2022, 5:45pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/4 "2022-06-02T17:45:51Z")
If you are restraining only the protein, are the amino acid residues in the beginning of the gro file? E.g., if there are 100K atoms (protein + water + ions + any other species) but your posres file has only 10K atoms, grompp will spit a message saying that only the first 10K atoms will be restrained. (you might have missed it if using -maxwarn). If that is the case, try renumbering the protein chain residues to appear at the beginning. Another point is: what is the force constant being used? Too small fc like 2 or 5 will be just too small to hold the protein. ---
**Author:** ![dkonstan](https://avatars.discourse-cdn.com/v4/letter/d/87869e/32.png) [@dkonstan](https://gromacs.bioexcel.eu/u/dkonstan)\ **Post date:** [June 2, 2022, 6:00pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/5 "2022-06-02T18:00:39Z")
On second thought, I have reason to believe the restraints ARE working, because when I take a system minimized with restrained protein and then try to run dynamics without minimizing the whole system first, the simulation crashes, but after I minimize everything things are fine. I just didn’t expect the atoms to move AT ALL when restrained, but I guess 1000 kj/mol is not that strong of a restraint, and that’s the default. It is probably ok that they vibrate a bit. Is that correct? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [June 2, 2022, 6:11pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/6 "2022-06-02T18:11:53Z")
> [@dkonstan](#): > > I just didn’t expect the atoms to move AT ALL when restrained, but I guess 1000 kj/mol is not that strong of a restraint, and that’s the default. It is probably ok that they vibrate a bit. Is that correct? Yes, a restraint penalizes motion. It doesn’t prevent it. ---
**Author:** ![dkonstan](https://avatars.discourse-cdn.com/v4/letter/d/87869e/32.png) [@dkonstan](https://gromacs.bioexcel.eu/u/dkonstan)\ **Post date:** [June 2, 2022, 6:16pm UTC](https://gromacs.bioexcel.eu/t/gromacs-not-reading-posres-even-though-it-is-pointed-to-in-topology/4255/7 "2022-06-02T18:16:28Z")
I am coming from mostly working with OpenMM where you often set your own restraints and I used to set them very high, probably a lot higher than is default in GROMACS, that’s why I had this misunderstanding. Thank you for helping me!