# Position restraints are not applied **URL:** \ **Category:** User discussions\ **Created:** [February 8, 2025, 5:40pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495 "2025-02-08T17:40:11Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![ehsank](https://avatars.discourse-cdn.com/v4/letter/e/977dab/32.png) [@ehsank](https://gromacs.bioexcel.eu/u/ehsank)\ **Post date:** [February 8, 2025, 5:40pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/1 "2025-02-08T17:40:11Z")
GROMACS version:gmx, 2022.1 GROMACS modification: No I am running an **equilibration simulation** (step6.3) using the **Dry Martini force field** in GROMACS, where I need to **apply position restraints** on the **headgroups of DOPC and cholesterol** in my vesicle system. I have done the following to enforce **position restraints** : 1. **Created `posre_dopc.itp` and `posre_chol.itp`** with force constants (`1000 1000 1000`). 2. **Included these files in `system.top`** using `#ifdef POSRES`. 3. **Defined `-DPOSRES` in `step6.3_equilibration.mdp`**. 4. **Checked that my `index.ndx` contains the correct groups (`DOPC_HEAD`, `CHOL_HEAD`)**. 5. **Ran `grompp` to generate `step6.3_equilibration.tpr`**. However, when I **check the `.tpr` file** using: gmx dump -s step6.3\_equilibration.tpr | grep posres I see that **position restraints are not applied** (`posres = 0.00000e+00` instead of `1000 1000 1000`). Despite setting everything correctly, **position restraints are missing in the `.tpr` file**. Could you suggest **how to debug and fix this issue**? Am I missing any step in **applying position restraints in Dry Martini systems?** Thank you for your guidance! ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [February 8, 2025, 8:27pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/2 "2025-02-08T20:27:03Z")
Hi @ehsank How are the constraints defined in the .itp files? Also as far as I know the restraints are independent from whatever you define in the index, as they are read from the topology if the keyword (`POSRES` in your case) is defined. ---
**Author:** ![ehsank](https://avatars.discourse-cdn.com/v4/letter/e/977dab/32.png) [@ehsank](https://gromacs.bioexcel.eu/u/ehsank)\ **Post date:** [February 8, 2025, 9:00pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/3 "2025-02-08T21:00:31Z")
Dear obZehn I have been working on applying position restraints on the headgroups of DOPC and cholesterol in my vesicle system using the Dry Martini force field in GROMACS. Below is a summary of my approach and the encountered issue: ### **Steps Taken:** 1. **Created Position Restraint Files:** - I generated `posre_dopc.itp` and `posre_chol.itp`, where I applied force constants of **1000 kJ/mol/nm²** on selected atoms extracted from `dopc_posres_atoms.txt` and `chol_posres_atoms.txt`. - Example entries: ```auto [position_restraints] ; i funct fcx fcy fcz 2 1 1000 1000 1000 14 1 1000 1000 1000 26 1 1000 1000 1000 ... ``` 1. **Modified `system.top` to Include Restraints:** - Used `#ifdef POSRES` to include the `.itp` files only when `-DPOSRES` is defined in the `.mdp` file. ```auto #ifdef POSRES #include "posre_dopc.itp" #include "posre_chol.itp" #endif ``` 1. **Ensured Correct Groups in `index.ndx`:** - Used `gmx make_ndx` to generate groups `DOPC_HEAD` and `CHOL_HEAD` and verified them. 1. **Checked the `.tpr` File for Restraints:** - After running: ```auto gmx dump -s step6.3_equilibration.tpr | grep posres ``` the output showed `posres = 0.00000e+00`, indicating that the restraints were not applied. ### **Issue and Diagnosis:** - **Error Message:** ```auto ERROR 1 [file posre_dopc_fixed.itp, line 5]: Atom index (14) in position_restraints out of bounds (1-12). ``` - This suggests that **the atom indices in `posre_dopc.itp` are incorrect** because Dry Martini represents DOPC molecules using only **12 beads** and CHOL molecules using **8 beads**. - The indices in my `.itp` file were extracted from the full system, not per molecule, causing the **index out-of-bounds error**. ---
**Author:** ![ehsank](https://avatars.discourse-cdn.com/v4/letter/e/977dab/32.png) [@ehsank](https://gromacs.bioexcel.eu/u/ehsank)\ **Post date:** [February 8, 2025, 9:26pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/4 "2025-02-08T21:26:53Z")
How generate itp file for CHOL and DOPC in dry martini when used corse grain? ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [February 9, 2025, 2:53pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/5 "2025-02-09T14:53:51Z")
The error you are getting is related to the fact that you have to define the restraints based on the molecule’s atoms within the molecule’s definition and not by referring to the whole box. For example, cholesterol will be defined in its topology as a molecule with 8 beads, so it will have 8 atoms [1-8], each one with a type, charge, etc. Now you have to define the position restraints with respect to THESE numbers (so the individual molecules), and not the whole box. As such, if say atom 2 of cholesterol and atom 3 of DOPC are their (beadified) heads, then your position restraints will look simply like this ```auto ; restraints for cholesterol head [position_restraints] ; i funct fcx fcy fcz 2 1 1000 1000 1000 ``` and ```auto ; restraints for DOPC head [position_restraints] ; i funct fcx fcy fcz 3 1 1000 1000 1000 ``` ---
**Author:** ![ehsank](https://avatars.discourse-cdn.com/v4/letter/e/977dab/32.png) [@ehsank](https://gromacs.bioexcel.eu/u/ehsank)\ **Post date:** [February 9, 2025, 4:44pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/6 "2025-02-09T16:44:01Z")
thank you so much for your considerataion for clarification, it is my system.top ; This file was generated by TS Back Mapping ; Include the Martini force field and necessary lipid files #include “dry\_martini\_v2.1.itp” ; Martini 2.1 force field #include “dry\_martini\_v2.1\_cholesterol.itp” ; Cholesterol specific parameters #include “dry\_martini\_v2.1\_lipids.itp” ; DOPC and other lipids [system] Expect a large membrane [molecules] ; domain 0 ; in the upper monolayer DOPC 1389 #ifdef POSRES #include “posre\_dopc.itp” #endif CHOL 926 #ifdef POSRES #include “posre\_chol.itp” #endif ; domain 0 ; in the lower monolayer DOPC 533 #ifdef POSRES #include “posre\_dopc.itp” #endif CHOL 355 #ifdef POSRES #include “posre\_chol.itp” #endif I got this error again : Command line: gmx grompp -f step6.3\_equilibration.mdp -o step6.3\_equilibration.tpr -c step6.2\_equilibration.gro -p system.top -n index.ndx NOTE 1 [file step6.3\_equilibration.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance \> 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file step6.3\_equilibration.mdp]: Setting tcoupl from ‘V-rescale’ to ‘no’. sd handles temperature coupling implicitly. See the documentation for more information on which parameters affect temperature for sd. Setting the LD random seed to -1470997761 Generated 0 of the 703 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type ‘DOPC’ WARNING 1 [file system.top, line 19]: Too few parameters on line (source file /admin/build/admin/rpms/frontera/BUILD/gromacs-2022.1/src/gromacs/gmxpreprocess/toppush.cpp, line 1900) WARNING 2 [file system.top, line 26]: Too few parameters on line (source file /admin/build/admin/rpms/frontera/BUILD/gromacs-2022.1/src/gromacs/gmxpreprocess/toppush.cpp, line 1900) WARNING 3 [file system.top, line 31]: Too few parameters on line (source file /admin/build/admin/rpms/frontera/BUILD/gromacs-2022.1/src/gromacs/gmxpreprocess/toppush.cpp, line 1900) * * * Program: gmx grompp, version 2022.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 703) Fatal error: number of coordinates in coordinate file (step6.2\_equilibration.gro, 33312) does not match topology (system.top, 16668) ## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) login2.frontera(1017)$ my step6.3\_equilibration.mdp is: ; Integrator and time settings define = -DPOSRES ; This enables the #ifdef POSRES directive in system.top integrator = sd ; Stochastic dynamics (SD) integrator for Dry Martini tinit = 0.0 dt = 0.03 ; Time step of 30 fs, typical for Martini simulations nsteps = 3000000 ; Run for 2 million steps (total time = 60 ns) ; Output control nstlog = 1000 nstenergy = 1000 nstxout-compressed = 1000 compressed-x-precision = 100 ; Neighbor searching settings cutoff-scheme = Verlet nstlist = 10 ; Update neighbor list every 10 steps rlist = 1.4 ; Neighbor list cutoff at 1.4 nm pbc = xyz verlet-buffer-tolerance = 0.005 ; Electrostatics and van der Waals settings epsilon\_r = 15 ; Relative permittivity for implicit solvent coulombtype = reaction-field rcoulomb = 1.2 ; Coulomb interactions cutoff at 1.2 nm vdw\_type = cutoff vdw-modifier = Potential-shift-verlet ; Smoothly shift van der Waals potential to zero rvdw = 1.2 ; Van der Waals cutoff at 1.2 nm ; No pressure coupling (NVT ensemble) Pcoupl = no ; No pressure coupling for implicit solvent ; Minimal T-coupling to satisfy GROMACS requirements tcoupl = v-rescale tc-grps = System tau\_t = 1.0 ; Minimal coupling constant ref\_t = 310 ; Target temperature for the dummy group ; Generate initial velocities if needed (only for equilibration) gen\_vel = yes gen\_temp = 310 gen\_seed = 0395104856 refcoord\_scaling = all I want impose position retrain for my head drop of CHOL and DOPC in my vesicle because when I run equilibration my vesicle has 2 bumper on it , I try by this way remove them . I used dry martini altho Best Regards Ehsan ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [February 9, 2025, 7:02pm UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/7 "2025-02-09T19:02:46Z")
Where did you get this .mdp file? I am not familiar with martini dry, so I can help you only partially. Please also refer to the [manual](https://manual.gromacs.org/documentation/2024.1/user-guide/mdp-options.html). Firstly, you get two notes. These are not fundamental problems, but are still telling you that something is not fully okay and GROMACS is handling the problem internally. Note 1 tells you that you are both setting `rlist` and `verlet-buffer-tolerance`, while generally one excludes the other. GROMACS is telling you that it is ignoring the `rlist` and using the `verlet-buffer-tolerance` value to calculate `rlist`. If you _know_ that you need an `rlist` of 1.4nm then you can force it by setting `verlet-buffer-tolerance=-1`. Since I don’t think this is the case, then you can comment off `rlist=1.4` as it is not used. Note 2 tells you that using the v-rescale thermostat is incorrect as you are requiring `integrator=sd`, which handles internally the temperature. If you need the `sd` integrator then you can set `tcoupl = no` or remove altogether the line, as this is the default. Otherwise, you integrate with `integrator = md` and you keep the v-rescale thermostat. Then you get three errors. It is hard to go through them as these are due to a incorrectly defined topology. You first start by defining the force field details and the molecules of interest with the respective restraints (as these are part of the individual molecular topology) and then you put the specifics of the `[system]` and the `[molecules]`. Try with something like this ```auto ; general force field definitions #include “dry_martini_v2.1.itp” ; definition of dopc #include “dry_martini_v2.1_lipids.itp" #ifdef POSRES #include “posre_dopc.itp” #endif ; definition of cholesterol #include “dry_martini_v2.1_cholesterol.itp” #ifdef POSRES #include “posre_chol.itp” #endif [system] Expect a large membrane [molecules] DOPC 1389 CHOL 926 DOPC 533 CHOL 355 ``` I think this still wont work as the `dry_martini_v2.1_lipids.itp` will include several lipid definitions and not only that of DOPC, so `grompp` will complain again. If that’s the case then you will have to modify the file and add these lines ```auto #ifdef POSRES #include “posre_dopcl.itp” #endif ``` to the very end of the DOPC molecule definition. It is very likely that these official lipid parameters will already have a restraint definition, though. ---
**Author:** ![ehsank](https://avatars.discourse-cdn.com/v4/letter/e/977dab/32.png) [@ehsank](https://gromacs.bioexcel.eu/u/ehsank)\ **Post date:** [February 10, 2025, 12:59am UTC](https://gromacs.bioexcel.eu/t/position-restraints-are-not-applied/11495/8 "2025-02-10T00:59:07Z")
Dear @obZehn Thank you so much for your consideration and your time, I will going to do that Best Regards Ehsan