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
My question is: I am not purturbing any mass or any constraint in my free energy calculations, so why do I get this error?