Tsjerk
commented
3 months ago The atomistic structure is rebuilt and matches the topology, given that the run starts. It may not be a backward error per se, but please send the files so I can have a better look: tsjerkw >At< gmail.com
Hello everyone,
After performing a CG Martini3 simulation, I wanted to re-atomize a snapshot of a trajectory frame for structural analysis. I've done this before using Martini2 but using the backward.py script on a Martini3 model results in multiple errors. The GROMACS energy minimization step within initram.sh results in a 'Segmentation fault' error and prevents the complete script execution. Any information to resolve this issue would be appreciated.
My command line input: ../bash initram.sh -f 644125ps.gro -o all_atom.gro -to charmm36 -p topol.top
Now executing...
initram.sh -f 644125ps.gro -o all_atom.gro -to charmm36 -p topol.top
GROMACS VERSION: MPI: false /mnt/c/users/julia/Desktop/Martini3_ex/backward.py -f 644125ps.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname SOL Error reading charmm27 to martini mapping for ALA (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/ala.gromos.map). Error reading charmm36 to martini mapping for ALA (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/ala.gromos.map). Error reading charmm27 to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map). Error reading charmm36 to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map). Error reading slipids to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map). Error reading amber to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map). Error reading charmm27 to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map). Error reading charmm36 to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map). Error reading slipids to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map). Error reading amber to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map). Error reading charmm36 to martini mapping for REYP (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/sep.gromos.map). Error reading charmm27 to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map). Error reading charmm36 to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map). Error reading slipids to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map). Error reading amber to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map). Error reading charmm to martini mapping for TOG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trehalose.gromos.map). Error reading charmm36 to martini mapping for TOG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trehalose.gromos.map). Error reading charmm27 to martini mapping for TRP (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trp.gromos.map). Error reading charmm36 to martini mapping for TRP (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trp.gromos.map). Error reading charmm27 to martini mapping for TYR (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tyr.gromos.map). Error reading charmm36 to martini mapping for TYR (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tyr.gromos.map). Residues defined for transformation from martini to charmm36: dict_keys(['A', 'ALA', 'ARG', 'ASN', 'ASP', 'C', 'CHOL', 'CYS', 'DA', 'DAT3', 'DAT5', 'DC', 'DCT3', 'DCT5', 'DG', 'DGT3', 'DGT5', 'DMPC', 'DOPC', 'DOPE', 'DOPG', 'DOPS', 'DPPC', 'DPPG', 'DT', 'DTT3', 'DTT5', 'G', 'GB3', 'Gb3', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'POPC', 'POPE', 'POPG', 'POPS', 'PRO', 'REYP', 'SER', 'THR', 'TOCL2', 'TOG', 'TRP', 'TYR', 'U', 'VAL']) None gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2 :-) GROMACS - gmx grompp, 2023 (-:
Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /mnt/c/users/julia/Desktop/Martini3_ex Command line: gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
Setting the LD random seed to -1778651149
Generated 168 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
WARNING 1 [file backmapped.top, line 134786]: The following macros were defined in the 'define' mdp field with the -D prefix, but were not used in the topology: FLEXIBLE If you haven't made a spelling error, either use the macro you defined, or don't define the macro
WARNING 2 [file backmapped.top, line 134786]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at https://gitlab.com/gromacs/gromacs/-/issues/2884, and a longer explanation of our decision to remove physically incorrect algorithms can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 .
NOTE 1 [file backmapped.top, line 134786]: System has non-zero total charge: 41.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer.
Number of degrees of freedom in T-Coupling group rest is 61308.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature
NOTE 2 [file 1-EM.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics.
This run will generate roughly 2 Mb of data
There were 2 NOTEs
There were 2 WARNINGs
GROMACS reminds you: "Given enough eyeballs, all bugs are shallow." (Linus Torvalds, on the power of open source)
gmx mdrun -deffnm 1-EM -v -nt 1 :-) GROMACS - gmx mdrun, 2023 (-:
Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /mnt/c/users/julia/Desktop/Martini3_ex Command line: gmx mdrun -deffnm 1-EM -v -nt 1
Reading file 1-EM.tpr, VERSION 2023 (single precision) 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 1 OpenMP thread
NOTE: Thread affinity was not set.
Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 500 Step= 0, Dmax= 1.0e-01 nm, Epot= 4.85033e+08 Fmax= 7.11856e+10, atom= 188 Step= 1, Dmax= 1.0e-01 nm, Epot= 8.89150e+07 Fmax= 9.04316e+08, atom= 9084 Step= 2, Dmax= 1.2e-01 nm, Epot= 3.55622e+07 Fmax= 1.72705e+07, atom= 4724 Step= 3, Dmax= 1.4e-01 nm, Epot= 2.14980e+07 Fmax= 4.20497e+06, atom= 4724 Step= 4, Dmax= 1.7e-01 nm, Epot= 1.47371e+07 Fmax= 9.96984e+05, atom= 15542 Step= 5, Dmax= 2.1e-01 nm, Epot= 6.67723e+06 Fmax= 1.70267e+06, atom= 8418 Step= 7, Dmax= 1.2e-01 nm, Epot= 5.62722e+06 Fmax= 3.36881e+05, atom= 5412 Step= 8, Dmax= 1.5e-01 nm, Epot= 4.37037e+06 Fmax= 7.70512e+05, atom= 18134 Step= 9, Dmax= 1.8e-01 nm, Epot= 3.88358e+06 Fmax= 4.81046e+05, atom= 18134 Step= 10, Dmax= 2.1e-01 nm, Epot= 3.53590e+06 Fmax= 2.36912e+05, atom= 3816 Step= 11, Dmax= 2.6e-01 nm, Epot= 3.01119e+06 Fmax= 8.37772e+05, atom= 14128 Step= 12, Dmax= 3.1e-01 nm, Epot= 2.55729e+06 Fmax= 1.49341e+05, atom= 14128 Step= 14, Dmax= 1.9e-01 nm, Epot= 2.23174e+06 Fmax= 6.38624e+05, atom= 13283 Step= 15, Dmax= 2.2e-01 nm, Epot= 1.96398e+06 Fmax= 1.33484e+05, atom= 4029 Step= 17, Dmax= 1.3e-01 nm, Epot= 1.75396e+06 Fmax= 7.36521e+05, atom= 8263 Step= 18, Dmax= 1.6e-01 nm, Epot= 1.61242e+06 Fmax= 1.51815e+05, atom= 6301 Step= 19, Dmax= 1.9e-01 nm, Epot= 1.59207e+06 Fmax= 4.86167e+05, atom= 6303 Step= 20, Dmax= 2.3e-01 nm, Epot= 1.30992e+06 Fmax= 2.45264e+05, atom= 18105 Step= 22, Dmax= 1.4e-01 nm, Epot= 1.23323e+06 Fmax= 2.60334e+06, atom= 18110 Step= 23, Dmax= 1.7e-01 nm, Epot= 1.17183e+06 Fmax= 2.26053e+05, atom= 18109 Step= 24, Dmax= 2.0e-01 nm, Epot= 1.11470e+06 Fmax= 4.05429e+05, atom= 13032 Step= 25, Dmax= 2.4e-01 nm, Epot= 1.07217e+06 Fmax= 3.29393e+05, atom= 13032 Step= 26, Dmax= 2.9e-01 nm, Epot= 9.60050e+05 Fmax= 4.28212e+05, atom= 13030 Step= 28, Dmax= 1.7e-01 nm, Epot= 8.92822e+05 Fmax= 4.39478e+05, atom= 2271 Step= 29, Dmax= 2.1e-01 nm, Epot= 8.57860e+05 Fmax= 2.09576e+06, atom= 2271 Step= 30, Dmax= 2.5e-01 nm, Epot= 8.43528e+05 Fmax= 9.02032e+05, atom= 2263 Step= 31, Dmax= 3.0e-01 nm, Epot= 7.93643e+05 Fmax= 1.23980e+05, atom= 5925 Step= 34, Dmax= 8.9e-02 nm, Epot= 7.15279e+05 Fmax= 1.78590e+05, atom= 9033 Step= 36, Dmax= 5.4e-02 nm, Epot= 7.10623e+05 Fmax= 1.35118e+05, atom= 12581 Step= 37, Dmax= 6.4e-02 nm, Epot= 6.41132e+05 Fmax= 1.23469e+05, atom= 1670 Step= 40, Dmax= 1.9e-02 nm, Epot= 6.11483e+05 Fmax= 1.37938e+05, atom= 16709 Step= 41, Dmax= 2.3e-02 nm, Epot= 5.85667e+05 Fmax= 1.71870e+05, atom= 17458 Step= 42, Dmax= 2.8e-02 nm, Epot= 5.42215e+05 Fmax= 1.41299e+05, atom= 13406 Step= 44, Dmax= 1.7e-02 nm, Epot= 4.94227e+05 Fmax= 1.41570e+05, atom= 52436 Step= 46, Dmax= 1.0e-02 nm, Epot= 4.53111e+05 Fmax= 9.38372e+05, atom= 14130 Step= 47, Dmax= 1.2e-02 nm, Epot= 4.36512e+05 Fmax= 1.37887e+05, atom= 15970 Step= 50, Dmax= 3.6e-03 nm, Epot= 4.24298e+05 Fmax= 1.36315e+06, atom= 13408 Step= 51, Dmax= 4.3e-03 nm, Epot= 4.19848e+05 Fmax= 1.34886e+05, atom= 11693 Step= 53, Dmax= 2.6e-03 nm, Epot= 4.12426e+05 Fmax= 5.69385e+05, atom= 7164 Step= 54, Dmax= 3.1e-03 nm, Epot= 4.07180e+05 Fmax= 1.27546e+05, atom= 11776 Step= 57, Dmax= 9.3e-04 nm, Epot= 4.03964e+05 Fmax= 2.25327e+05, atom= 15972 Step= 58, Dmax= 1.1e-03 nm, Epot= 4.00012e+05 Fmax= 4.63011e+05, atom= 15973 Step= 59, Dmax= 1.3e-03 nm, Epot= 3.98764e+05 Fmax= 9.26642e+04, atom= 11946 Step= 63, Dmax= 2.0e-04 nm, Epot= 3.97455e+05 Fmax= 1.95939e+05, atom= 12370 Step= 64, Dmax= 2.4e-04 nm, Epot= 3.96943e+05 Fmax= 2.38277e+05, atom= 18383 Step= 65, Dmax= 2.9e-04 nm, Epot= 3.96496e+05 Fmax= 1.59611e+05, atom= 11778 Step= 67, Dmax= 1.7e-04 nm, Epot= 3.96012e+05 Fmax= 1.88325e+05, atom= 11778 Step= 68, Dmax= 2.1e-04 nm, Epot= 3.95800e+05 Fmax= 2.14286e+05, atom= 12369 Step= 69, Dmax= 2.5e-04 nm, Epot= 3.95536e+05 Fmax= 7.45955e+05, atom= 16954 initram.sh: line 372: 129 Segmentation fault $M gmx grompp -f 2-EM.mdp -c 1-EM.gro -n backmapped.ndx -p backmapped.top -o 2-EM -maxwarn 2 :-) GROMACS - gmx grompp, 2023 (-:
Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /mnt/c/users/julia/Desktop/Martini3_ex Command line: gmx grompp -f 2-EM.mdp -c 1-EM.gro -n backmapped.ndx -p backmapped.top -o 2-EM -maxwarn 2
Program: gmx grompp, version 2023 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271) Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input: Invalid command-line options In command-line option -c File '1-EM.gro' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors