# Fatal error: Perturbed masses or constraints are not supported by rerun **URL:** \ **Category:** User discussions\ **Tags:** mdrun, free-energy\ **Created:** [September 9, 2024, 10:04pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-perturbed-masses-or-constraints-are-not-supported-by-rerun/10133 "2024-09-09T22:04:02Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![swapnilw](https://avatars.discourse-cdn.com/v4/letter/s/b38774/32.png) [@swapnilw](https://gromacs.bioexcel.eu/u/swapnilw)\ **Post date:** [September 9, 2024, 10:04pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-perturbed-masses-or-constraints-are-not-supported-by-rerun/10133/1 "2024-09-09T22:04:02Z")
GROMACS version: 2022 GROMACS modification: No Here post your question Hi, I have run a solvation free energy calculation using non-equilibrium free enregy simulations. I am experimenting with the mdp parameters and recalculating the dhdl.xvg file using the `-rerun` option. I have run a non-equilibrium simulation with the following free energy parameters in my mdp file: free-energy = yes sc-function = gapsys init\_lambda = 0 delta\_lambda = 0.000004 ;1/nsteps define = -DLIGAND\_AB In this non-eq FE perturbration, my aim is to only perturb the vdw and charges of the atoms, and the atoms section of my topology looks like: [moleculetype] ; Name nrexcl LIG 3 [atoms] #ifdef LIGAND\_AB 1 C3dC1 1 LIG C1x 1 -0.099380 12.0108 C5dC1 -0.097890 12.0108 2 C3dC2 1 LIG C2x 2 -0.130510 12.0108 C5dC2 -0.118160 12.0108 3 C3dC3 1 LIG C3x 3 -0.106030 12.0108 C5dC3 -0.113530 12.0108 4 C3dC4 1 LIG C4x 4 -0.162570 12.0108 C5dC4 -0.155770 12.0108 5 C3dC5 1 LIG C5x 5 0.378230 12.0108 C5dC5 0.330390 12.0108 6 C3dN6 1 LIG N1x 6 -0.381160 14.0067 C5dN6 -0.281810 14.0067 7 C3dN7 1 LIG N2x 7 0.062510 14.0067 C5dN7 -0.245480 14.0067 8 C3dN8 1 LIG N3x 8 -0.472830 14.0067 C5dC8 0.336240 12.0108 9 C3dC9 1 LIG C6x 9 0.680910 12.0108 C5dC9 0.122460 12.0108 10 C3dC10 1 LIG C7x 10 -0.280120 12.0108 C5dC10 -0.122950 12.0108 11 C3dN11 1 LIG N4x 11 -0.857370 14.0067 C5dN11 -0.746030 14.0067 12 C3dC12 1 LIG C8x 12 0.212180 12.0108 C5dC12 0.183430 12.0108 13 C3dC13 1 LIG C9x 13 -0.094180 12.0108 C5dC13 -0.083950 12.0108 14 C3dC14 1 LIG C10x 14 -0.080580 12.0108 C5dC14 -0.078010 12.0108 15 C3dC15 1 LIG C11x 15 0.029790 12.0108 C5dC15 0.029720 12.0108 16 C3dC16 1 LIG C12x 16 -0.124850 12.0108 C5dC16 -0.124670 12.0108 17 C3dC17 1 LIG C13x 17 -0.127980 12.0108 C5dC17 -0.127810 12.0108 18 C3dC18 1 LIG C14x 18 -0.128050 12.0108 C5dC18 -0.128230 12.0108 19 C3dC19 1 LIG C15x 19 -0.127980 12.0108 C5dC21 -0.127810 12.0108 20 C3dC20 1 LIG C16x 20 -0.124850 12.0108 C5dC22 -0.124670 12.0108 21 C3dC21 1 LIG C17x 21 -0.080580 12.0108 C5dC23 -0.078010 12.0108 22 C3dC22 1 LIG C18x 22 -0.124850 12.0108 C5dC24 -0.124670 12.0108 23 C3dC23 1 LIG C19x 23 -0.127980 12.0108 C5dC25 -0.127810 12.0108 24 C3dC24 1 LIG C20x 24 -0.128050 12.0108 C5dC26 -0.128230 12.0108 25 C3dC25 1 LIG C21x 25 -0.127980 12.0108 C5dC27 -0.127810 12.0108 26 C3dC26 1 LIG C22x 26 -0.124850 12.0108 C5dC28 -0.124670 12.0108 27 C3dH27 1 LIG H1x 27 0.126770 1.0079 C5dH29 0.154920 1.0079 28 C3dH28 1 LIG H2x 28 0.140640 1.0079 C5dH30 0.144990 1.0079 29 C3dH29 1 LIG H3x 29 0.140860 1.0079 C5dH31 0.142510 1.0079 30 C3dH30 1 LIG H4x 30 0.159450 1.0079 C5dH32 0.157990 1.0079 31 C3dH31 1 LIG H5x 31 0.437630 1.0079 C5dH33 0.397820 1.0079 32 C3dH32 1 LIG H6x 32 0.067570 1.0079 C5dH34 0.047920 1.0079 33 C3dH33 1 LIG H7x 33 0.067570 1.0079 C5dH35 0.047920 1.0079 34 C3dH34 1 LIG H8x 34 0.053890 1.0079 C5dH36 0.056910 1.0079 35 C3dH35 1 LIG H9x 35 0.053890 1.0079 C5dH37 0.056910 1.0079 36 C3dH36 1 LIG H10x 36 0.067160 1.0079 C5dH38 0.061020 1.0079 37 C3dH37 1 LIG H11x 37 0.134170 1.0079 C5dH39 0.132640 1.0079 38 C3dH38 1 LIG H12x 38 0.132860 1.0079 C5dH40 0.132470 1.0079 39 C3dH39 1 LIG H13x 39 0.132780 1.0079 C5dH41 0.132670 1.0079 40 C3dH40 1 LIG H14x 40 0.132860 1.0079 C5dH42 0.132470 1.0079 41 C3dH41 1 LIG H15x 41 0.134170 1.0079 C5dH43 0.132640 1.0079 42 C3dH42 1 LIG H16x 42 0.134170 1.0079 C5dH44 0.132640 1.0079 43 C3dH43 1 LIG H17x 43 0.132860 1.0079 C5dH45 0.132470 1.0079 44 C3dH44 1 LIG H18x 44 0.132780 1.0079 C5dH46 0.132670 1.0079 45 C3dH45 1 LIG H19x 45 0.132860 1.0079 C5dH47 0.132470 1.0079 46 C3dH46 1 LIG H20x 46 0.134170 1.0079 C5dH48 0.132640 1.0079 47 DUM\_C5dC19 1 LIG DC16x 47 0.000000 12.0108 C5dC19 0.137520 12.0108 48 DUM\_C5dN20 1 LIG DN4x 48 0.000000 14.0067 C5dN20 -0.346480 14.0067 #endif I want to run a `-rerun` command on the trajectory file (traj\_comp.xtc) I just generated using my .tpr file (topol.tpr). But, when I run `gmx mdrun -s topol.tpr -rerun traj_comp.xtc` command, I get the following error: * * * Program: gmx mdrun, version 2022.1 Source file: src/gromacs/mdrun/rerun.cpp (line 207) Fatal error: Perturbed masses or constraints are not supported by rerun. Either make a .tpr without mass and constraint perturbation, or use GROMACS 2018.4, 2018.5 or later 2018 version. ## 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) My question is: I am not purturbing any mass or any constraint in my free energy calculations, so why do I get this error? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 10, 2024, 6:46am UTC](https://gromacs.bioexcel.eu/t/fatal-error-perturbed-masses-or-constraints-are-not-supported-by-rerun/10133/2 "2024-09-10T06:46:04Z")
Thanks, at a glance this looks like a bug. Does it work in 2024.3? If it doesn’t work there either, it would be great if you could write a bug report (preferably including necessary files to reproduce it) at [Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues/).