# LINCS warning and segmentation fault @ non-equilibrium part of simulation **URL:** \ **Category:** pmx\ **Created:** [December 2, 2024, 3:22pm UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352 "2024-12-02T15:22:09Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![tkoh](https://avatars.discourse-cdn.com/v4/letter/t/a9adbd/32.png) [@tkoh](https://ask.bioexcel.eu/u/tkoh)\ **Post date:** [December 2, 2024, 3:22pm UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/1 "2024-12-02T15:22:09Z")
Hi everyone, So I am trying to do free energy calculations for a mutant (M205A) with the human Prion protein (1QLX). However I keep running into a lincs warning at the non equilirium phase of the free energy simulation. The simulation is executed through a framework I created but incorporates the same steps as this tutorial ([Protein mutation — pmx documentation](https://degrootlab.github.io/pmx/tutorials/protein_mut.html)). Below is the output for the folded state non-equilibrium part (The whole output was too long for this post but essentially the commands are repeated per frame that is extracted), the MDP files ``` :-) GROMACS - gmx grompp, 2023.2 (-: ``` Executable: /usr/local/gromacs/bin/gmx\_mpi Data prefix: /usr/local/gromacs Working dir: /home/21616019/git\_projects/v5/PSA\_framework/work/d5/eca632fcf7c6986caf04f9e062bb0a/scratch/nxf.lXHjGvJx22/frame4 Command line: gmx\_mpi grompp -f …/r\_nonequil.mdp -c frame.gro -p …/newtop.top -o nonequil.tpr -maxwarn 1 Ignoring obsolete mdp entry ‘ns-type’ NOTE 1 [file …/r\_nonequil.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 0.0e+00, while ewald-rtol is 1.0e-05. Generating 1-4 interactions: fudge = 1 Number of degrees of freedom in T-Coupling group System is 50060.00 There was 1 NOTE GROMACS reminds you: “I admired Bohr very much. We had long talks together, long talks in which Bohr did practically all the talking.” (Paul Dirac) Setting the LD random seed to -2097415 Generated 118802 of the 118828 non-bonded parameter combinations Generated 88948 of the 118828 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_P’ turning H bonds into constraints… Excluding 2 bonded neighbours molecule type ‘SOL’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘NA’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘CL’ turning H bonds into constraints… Analysing residue names: There are: 104 Protein residues There are: 7608 Water residues There are: 49 Ion residues Analysing Protein… The largest distance between non-perturbed excluded atoms is 0.432 nm between atom 463 and 470 Determining Verlet buffer for a tolerance of 0.00025 kJ/mol/ps at 298.15 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.201 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 60x60x60, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.29 This run will generate roughly 7 Mb of data 🙂 GROMACS - gmx mdrun, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmx\_mpi Data prefix: /usr/local/gromacs Working dir: /home/21616019/git\_projects/v5/PSA\_framework/work/d5/eca632fcf7c6986caf04f9e062bb0a/scratch/nxf.lXHjGvJx22/frame4 Command line: gmx\_mpi mdrun -s nonequil.tpr -deffnm nonequil -dhdl dgdl\_rev4.xvg -v Compiled SIMD is AVX2\_256, but CPU also supports AVX\_512 (see log). Reading file nonequil.tpr, VERSION 2023.2 (single precision) Changing nstlist from 10 to 100, rlist from 1.201 to 1.249 Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms Using 1 MPI process Using 72 OpenMP threads starting mdrun ‘PMX MODEL in water’ 40000 steps, 8.0 ps. step 0 Step 1, time 0.0002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.918139, max 82.985596 (between atoms 1295 and 1298) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1295 1296 90.0 0.1110 0.1288 0.1111 1295 1297 90.0 0.1110 0.1288 0.1111 1295 1298 81.3 0.1110 9.3308 0.1111 1284 1285 90.0 0.0996 0.9370 0.0997 Wrote pdb files with previous and current coordinates Step 1, time 0.0002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.827562, max 80.210556 (between atoms 1295 and 1298) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1295 1296 90.0 0.1110 0.5256 0.1111 1295 1297 90.0 0.1110 0.5243 0.1111 1295 1298 129.3 0.1110 9.0225 0.1111 1284 1285 90.0 0.0996 0.9369 0.0997 Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1# Wrote pdb files with previous and current coordinates WARNING: Listed nonbonded interaction between particles 1291 and 1298 at distance 9.392 which is larger than the table limit 2.249 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. [n06:02481] \*\*\* Process received signal \*\*\* [n06:02481] Signal: Segmentation fault (11) [n06:02481] Signal code: Invalid permissions (2) [n06:02481] Failing at address: 0x7f3792421d88 [n06:02481] [0] /lib/x86\_64-linux-gnu/libc.so.6(+0x42520)[0x7f4b5f5bb520] [n06:02481] [1] /usr/local/gromacs/bin/…/lib/libgromacs\_mpi.so.8(+0xe1d67b)[0x7f4b6094967b] [n06:02481] [2] /lib/x86\_64-linux-gnu/libgomp.so.1(+0x1dc0e)[0x7f4b5f465c0e] [n06:02481] [3] /lib/x86\_64-linux-gnu/libc.so.6(+0x94ac3)[0x7f4b5f60dac3] [n06:02481] [4] /lib/x86\_64-linux-gnu/libc.so.6(clone+0x44)[0x7f4b5f69ea04] [n06:02481] \*\*\* End of error message \*\*\* /home/21616019/git\_projects/v5/PSA\_framework/work/d5/eca632fcf7c6986caf04f9e062bb0a/.command.sh: line 9: 2481 Segmentation fault (core dumped) gmx\_mpi mdrun -s nonequil.tpr -deffnm nonequil -dhdl dgdl\_rev$i.xvg -v. MDP Non-equilibrium reverse: ;==================================================== ; Non-equilibrium transition ;==================================================== ; RUN CONTROL ;---------------------------------------------------- integrator = sd ; stochastic leap-frog integrator nsteps = 40000 ; 2 \* 40000 fs = 80 ps dt = 0.0002 ; 2 fs comm-mode = Linear ; remove center of mass translation nstcomm = 1 ; frequency for center of mass motion removal ; OUTPUT CONTROL ;---------------------------------------------------- nstxout = 10000 ; save coordinates to .trr every 20 ps nstvout = 10000 ; save velocities to .trr every 20 ps nstfout = 10000 ; save forces to .trr every 20 ps nstxout-compressed = 10000 ; xtc compressed trajectory output every 20 ps compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file nstlog = 5000 ; update log file every 10 ps nstenergy = 1000 ; save energies every 2 ps nstcalcenergy = 1 ; calculate energies at every step ; BONDS ;---------------------------------------------------- constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; constrain H-bonds lincs-iter = 1 ; accuracy of LINCS (1 is default) lincs-order = 6 ; also related to accuracy (4 is default) lincs-warnangle = 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default) continuation = yes ; formerly known as ‘unconstrained-start’ - useful for exact continuations and reruns ; NEIGHBOR SEARCHING ;---------------------------------------------------- cutoff-scheme = Verlet ; group or Verlet ns-type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs (default is 10) rlist = 1.2 ; short-range neighborlist cutoff (in nm) pbc = xyz ; 3D PBC ; ELECTROSTATICS & EWALD ;---------------------------------------------------- coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics coulomb-modifier = Potential-shift-Verlet rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ewald-geometry = 3d ; Ewald sum is performed in all three dimensions pme-order = 4 ; interpolation order for PME (default is 4) fourierspacing = 0.12 ; grid spacing for FFT ewald-rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential at rcoulomb ; VAN DER WAALS ;---------------------------------------------------- vdw-type = Cut-off ; potential switched off at rvdw-switch to reach zero at rvdw vdw-modifier = force-switch verlet-buffer-tolerance = 0.00025 rvdw = 1.2 ; van der Waals cutoff (in nm) rvdw-switch = 1.0 DispCorr = no ; apply analytical long range dispersion corrections for Energy and Pressure ; TEMPERATURE COUPLING (Langevin) ;---------------------------------------------------- tc-grps = System tau-t = 1.0 ref-t = 298.15 gen-vel = no ; Velocity generation (if gen-vel is ‘yes’, continuation should be ‘no’) gen-seed = -1 ; PRESSURE COUPLING ;---------------------------------------------------- pcoupl = C-rescale pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant (ps) ref\_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) refcoord-scaling = no ; FREE ENERGY ;---------------------------------------------------- free-energy = yes init-lambda = 1 ; start from state B delta-lambda = -2.5e-05 ; complete transition in this number of steps sc-coul = yes ; use soft-core also for coulombic interactions sc-alpha = 0 ; soft-core sc-sigma = 0.34 ; sc-power = 1 ; nstdhdl = 1 ; write to dhdl at each step The same also occurs for my tripeptide M2A. ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [December 2, 2024, 4:14pm UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/2 "2024-12-02T16:14:44Z")
You need to switch soft-core on, e.g. sc-alpha = 0.3 ---
**Author:** ![tkoh](https://avatars.discourse-cdn.com/v4/letter/t/a9adbd/32.png) [@tkoh](https://ask.bioexcel.eu/u/tkoh)\ **Post date:** [December 4, 2024, 8:52am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/3 "2024-12-04T08:52:57Z")
So I have switched on the soft-core for non-equilibrium and it works in the sense where I don’t get a segmentation fault and the command runs to completion however it does result in a warning that occurs. Also wanted to know if the note presented below is a cause for concern. Below is the output and MDP file: 🙂 GROMACS - gmx trjconv, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmx\_mpi Data prefix: /usr/local/gromacs Working dir: /home/21616019/git\_projects/v5/PSA\_framework/work/5c/854c2e4ff34c252a3f48c663390378/scratch/nxf.rIzrYHGlPV Command line: gmx\_mpi trjconv -f equil.trr -s equil.tpr -sep -b 100 -o frame\_.gro Will write gro: Coordinate file in Gromos-87 format Reading file equil.tpr, VERSION 2023.2 (single precision) Reading file equil.tpr, VERSION 2023.2 (single precision) Group 0 ( System) has 24568 elements Group 1 ( Protein) has 1695 elements Group 2 ( Protein-H) has 878 elements Group 3 ( C-alpha) has 104 elements Group 4 ( Backbone) has 312 elements Group 5 ( MainChain) has 415 elements Group 6 ( MainChain+Cb) has 514 elements Group 7 ( MainChain+H) has 518 elements Group 8 ( SideChain) has 1177 elements Group 9 ( SideChain-H) has 463 elements Group 10 ( Prot-Masses) has 1695 elements Group 11 ( non-Protein) has 22873 elements Group 12 ( Water) has 22824 elements Group 13 ( SOL) has 22824 elements Group 14 ( non-Water) has 1744 elements Group 15 ( Ion) has 49 elements Group 16 ( Water\_and\_ions) has 22873 elements Select a group: trr version: GMX\_trn\_file (single precision) Skipping frame 0 time 0.000 Reading frame 1 time 100.000 Reading frame 2 time 200.000 → frame 0 time 100.000 Reading frame 3 time 300.000 → frame 1 time 200.000 Reading frame 4 time 400.000 → frame 2 time 300.000 Reading frame 5 time 500.000 → frame 3 time 400.000 Reading frame 6 time 600.000 → frame 4 time 500.000 Reading frame 7 time 700.000 → frame 5 time 600.000 Reading frame 8 time 800.000 → frame 6 time 700.000 Reading frame 9 time 900.000 → frame 7 time 800.000 Reading frame 10 time 1000.000 → frame 8 time 900.000 Reading frame 11 time 1100.000 → frame 9 time 1000.000 Reading frame 12 time 1200.000 → frame 10 time 1100.000 Reading frame 13 time 1300.000 → frame 11 time 1200.000 Reading frame 14 time 1400.000 → frame 12 time 1300.000 Reading frame 15 time 1500.000 → frame 13 time 1400.000 Reading frame 16 time 1600.000 → frame 14 time 1500.000 Reading frame 17 time 1700.000 → frame 15 time 1600.000 Reading frame 18 time 1800.000 → frame 16 time 1700.000 Reading frame 19 time 1900.000 → frame 17 time 1800.000 Reading frame 20 time 2000.000 → frame 18 time 1900.000 Reading frame 30 time 3000.000 → frame 28 time 2900.000 Reading frame 40 time 4000.000 → frame 38 time 3900.000 Reading frame 50 time 5000.000 → frame 48 time 4900.000 Last frame 50 time 5000.000 → frame 49 time 5000.000 Last written: frame 49 time 5000.000 GROMACS reminds you: “Quite frankly, even if the choice of C were to do _nothing_ but keep the C++ programmers out, that in itself would be a huge reason to use C.” (Linus Torvalds) Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 0: ‘System’ 🙂 GROMACS - gmx grompp, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmx\_mpi Data prefix: /usr/local/gromacs Working dir: /home/21616019/git\_projects/v5/PSA\_framework/work/5c/854c2e4ff34c252a3f48c663390378/scratch/nxf.rIzrYHGlPV/frame1 Command line: gmx\_mpi grompp -f …/f\_nonequil.mdp -c frame.gro -p …/newtop.top -o nonequil.tpr -maxwarn 1 Ignoring obsolete mdp entry ‘ns-type’ WARNING 1 [file …/f\_nonequil.mdp, line 87]: You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0. NOTE 1 [file …/f\_nonequil.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 1.3e-05, while ewald-rtol is 1.0e-05. Generating 1-4 interactions: fudge = 1 Number of degrees of freedom in T-Coupling group System is 50060.00 There was 1 NOTE There was 1 WARNING GROMACS reminds you: “Come on boys, Let’s push it hard” (P.J. Harvey) Setting the LD random seed to -1292046657 Generated 118802 of the 118828 non-bonded parameter combinations Generated 88948 of the 118828 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_P’ turning H bonds into constraints… Excluding 2 bonded neighbours molecule type ‘SOL’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘NA’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘CL’ turning H bonds into constraints… Analysing residue names: There are: 104 Protein residues There are: 7608 Water residues There are: 49 Ion residues Analysing Protein… The largest distance between non-perturbed excluded atoms is 0.445 nm between atom 886 and 1441 Determining Verlet buffer for a tolerance of 0.00025 kJ/mol/ps at 298.15 K Calculated rlist for 1x1 atom pair-list as 1.202 nm, buffer size 0.002 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 60x60x60, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.29 This run will generate roughly 7 Mb of data MDP: ;==================================================== ; Non-equilibrium transition ;==================================================== ; RUN CONTROL ;---------------------------------------------------- integrator = sd ; stochastic leap-frog integrator nsteps = 40000 ; 2 \* 40000 fs = 80 ps dt = 0.0001 ; 2 fs comm-mode = Linear ; remove center of mass translation nstcomm = 1 ; frequency for center of mass motion removal ; OUTPUT CONTROL ;---------------------------------------------------- nstxout = 10000 ; save coordinates to .trr every 20 ps nstvout = 10000 ; save velocities to .trr every 20 ps nstfout = 10000 ; save forces to .trr every 20 ps nstxout-compressed = 10000 ; xtc compressed trajectory output every 20 ps compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file nstlog = 5000 ; update log file every 10 ps nstenergy = 1000 ; save energies every 2 ps nstcalcenergy = 1 ; calculate energies at every step ; BONDS ;---------------------------------------------------- constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; constrain H-bonds lincs-iter = 1 ; accuracy of LINCS (1 is default) lincs-order = 6 ; also related to accuracy (4 is default) lincs-warnangle = 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default) continuation = yes ; formerly known as ‘unconstrained-start’ - useful for exact continuations and reruns ; NEIGHBOR SEARCHING ;---------------------------------------------------- cutoff-scheme = Verlet ; group or Verlet ns-type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs (default is 10) rlist = 1.2 ; short-range neighborlist cutoff (in nm) pbc = xyz ; 3D PBC ; ELECTROSTATICS & EWALD ;---------------------------------------------------- coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics coulomb-modifier = Potential-shift-Verlet rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ewald-geometry = 3d ; Ewald sum is performed in all three dimensions pme-order = 4 ; interpolation order for PME (default is 4) fourierspacing = 0.12 ; grid spacing for FFT ewald-rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential at rcoulomb ; VAN DER WAALS ;---------------------------------------------------- vdw-type = Cut-off ; potential switched off at rvdw-switch to reach zero at rvdw vdw-modifier = force-switch verlet-buffer-tolerance = 0.00025 rvdw = 1.2 ; van der Waals cutoff (in nm) rvdw-switch = 1.0 DispCorr = no ; apply analytical long range dispersion corrections for Energy and Pressure ; TEMPERATURE COUPLING (Langevin) ;---------------------------------------------------- tc-grps = System tau-t = 1.0 ref-t = 298.15 gen-vel = no ; Velocity generation (if gen-vel is ‘yes’, continuation should be ‘no’) gen-seed = -1 ; PRESSURE COUPLING ;---------------------------------------------------- pcoupl = C-rescale pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant (ps) ref\_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) refcoord-scaling = no ; FREE ENERGY ;---------------------------------------------------- free-energy = yes init-lambda = 0 ; start from state A delta-lambda = 2.5e-05 ; complete transition in this number of steps sc-coul = yes ; use soft-core also for coulombic interactions sc-alpha = 0.3 ; soft-core sc-sigma = 0.34 ; sc-power = 1 ; nstdhdl = 1 ; write to dhdl at each step Another question I have is why does a segmentation fault occur only for the reverse transformation when soft-core if off? What impact does it have? ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [December 4, 2024, 9:18am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/4 "2024-12-04T09:18:42Z")
This warning is safe to ignore. As the note says, the effect will be very minor and the noise from other effects will be larger. You see the effect of softcore in one direction only probably because you have more non-dummy atoms in stateA and they cause clashes with other real atoms in the system when going from B to A. ---
**Author:** ![tkoh](https://avatars.discourse-cdn.com/v4/letter/t/a9adbd/32.png) [@tkoh](https://ask.bioexcel.eu/u/tkoh)\ **Post date:** [December 6, 2024, 10:02am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/5 "2024-12-06T10:02:09Z")
Thank you so much for your responses. Another query on an error, so although the above errors were solved, the same parameters were applied to the tripeptide G2V and the result was an additional warning: Command error: Ignoring obsolete mdp entry ‘ns-type’ WARNING 1 [file …/r\_nonequil.mdp, line 87]: You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0. NOTE 1 [file …/r\_nonequil.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 1.3e-05, while ewald-rtol is 1.0e-05. Generating 1-4 interactions: fudge = 1 WARNING 2 [file tripep\_G2V.top, line 17]: The bond in molecule-type Protein\_chain\_X between atoms 22 DCG1 and 23 DHG1 has an estimated oscillational period of 8.6e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 6014.00 There was 1 NOTE There were 2 WARNINGs The h-bonds are contrained, and I can reduce the time step, however the reduced time step would apply to both the tripeptide and the folded structure. And I am not sure of the effect this will have. ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [December 7, 2024, 11:27am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/6 "2024-12-07T11:27:28Z")
It seems you are using ‘master’ branch of pmx: with it only all-bond constraints are supported. h-bond constraints are supported with the ‘develop’ branch of pmx ---
**Author:** ![tkoh](https://avatars.discourse-cdn.com/v4/letter/t/a9adbd/32.png) [@tkoh](https://ask.bioexcel.eu/u/tkoh)\ **Post date:** [December 7, 2024, 11:30am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/7 "2024-12-07T11:30:41Z")
I am using the develop branch of PMX, the simulation with the M205A mutation with H-bond constraints ran successfully. However the G127V gives the warning about oscillation period. ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [December 9, 2024, 8:12am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352/8 "2024-12-09T08:12:00Z")
Could you make sure that you are using amber99sb-star-ildn-mut.ff, amber14sbmut.ff or charmm36m-mut.ff in the ‘develop’ branch? There is no atom type DHG1 defined for these force fields