Dear all,

trying to run a 'polymer blend' system. Have generated a 200 atom ish topoology for each polymer using polypargen giving me A,B polymers, then have coarse grained them myself and used pyCGtool to generate the bond angles etc..

at the point of running them together and is now beginning to fail. When I run x10 polymers in a box it runs fine for 100 ns, then when I add second in it begins to fail.

example of my input procedure is below, evertything minimizes to an extent but LINCS errors on npt run (shown below)

have tried making the box bigger, increasing the time step and have used GMX_MAXCONSTRWARN to -1 but this led to problems with the pressure

if there is anything you can advise that would be great !

many thanks in advance

---

gmx editconf -f out.gro -o box.gro -box 6 6 6
gmx insert-molecules -f box.gro -ci out.gro -o new_box.gro -nmol 9

gmx grompp -f em.mdp -c new_box.gro -p topol.top -o em.tpr -maxwarn 10

gmx mdrun -deffnm em -v

gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr -maxwarn 10

gmx mdrun -deffnm npt -v

---

gmx insert-molecules -f new_box.gro -ci mpa.gro -o full_box.gro -nmol 10


gmx grompp -f em.mdp -c new_box.gro -p topol.top -o em.tpr -maxwarn 10

gmx mdrun -deffnm em -v

gmx insert-molecules -f new_box.gro -ci mpa.gro -o full_box.gro -nmol 10

gmx mdrun -deffnm npt -v

---

npt.mdp

;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.

title = Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.

integrator = md
dt = 0.01
nsteps = 10000000
nstcomm = 100
comm-grps =

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-grps =
energygrps = System

; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to
; do so, the cutoff distance is reduced 1.1 nm.
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.


cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
;
; Pressure can be controlled with the Parrinello-Rahman barostat,
; with a coupling constant in the range 4-8 ps and typical compressibility
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes,
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure
; coupling should be done semiisotropic.

tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 310
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4
ref_p = 1.0
refcoord_scaling = all

gen_vel = no

; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints = none
constraint_algorithm = Lincs

---

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54

---

---

--- Thank You ---

---

---

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447

---

---

--- Thank You ---

---

---

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719

---

---

--- Thank You ---

---

---

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317

---

---

--- Thank You ---

---

---

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56

---

---

--- Thank You ---

---

---

++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
doi.org/10.5281/zenodo.3773801

---

---

--- Thank You ---

---

---

Input Parameters:
integrator = md
tinit = 0
dt = 0.01
nsteps = 10000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -1939064558
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100
cutoff-scheme = Verlet
nstlist = 20
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 1.1
coulombtype = Reaction-Field
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 15
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1.1
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
tcoupl = V-rescale
nsttcouple = 20
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = Berendsen
pcoupltype = Isotropic
nstpcouple = 20
tau-p = 12
compressibility (3x3):
compressibility[ 0]={ 3.00000e-04, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 3.00000e-04, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 3.00000e-04}
ref-p (3x3):
ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
refcoord-scaling = All
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
QMMM = false
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = false
Shake-SOR = false
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = false
awh = false
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
simulated-tempering = false
swapcoords = no
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
applied-forces:
electric-field:
x:
E0 = 0
omega = 0
t0 = 0
sigma = 0
y:
E0 = 0
omega = 0
t0 = 0
sigma = 0
z:
E0 = 0
omega = 0
t0 = 0
sigma = 0
density-guided-simulation:
active = false
group = protein
similarity-measure = inner-product
atom-spreading-weight = unity
force-constant = 1e+09
gaussian-transform-spreading-width = 0.2
gaussian-transform-spreading-range-in-multiples-of-width = 4
reference-density-filename = reference.mrc
nst = 1
normalize-densities = true
adaptive-force-scaling = false
adaptive-force-scaling-time-constant = 4
grpopts:
nrdf: 1307
ref-t: 310
tau-t: 1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0

Changing nstlist from 20 to 100, rlist from 1.1 to 1.1

Using 1 MPI thread

Non-default thread affinity set, disabling internal thread affinity

Using 4 OpenMP threads

System total charge: 0.000
Reaction-Field:
epsRF = 0, rc = 1.1, krf = 0.375657, crf = 1.36364, epsfac = 9.26236
The electrostatics potential has its minimum at r = 1.1
Potential shift: LJ r^-12: -3.186e-01 r^-6: -5.645e-01

Using SIMD 4x8 nonbonded short-range kernels

Using a 4x8 pair-list setup:
updated every 100 steps, buffer 0.000 nm, rlist 1.100 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
updated every 100 steps, buffer 0.000 nm, rlist 1.100 nm

Using full Lennard-Jones parameter combination matrix

Removing pbc first time

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122

---

---

--- Thank You ---

---

---

The number of constraints is 130
90 constraints are involved in constraint triangles,
will apply an additional matrix expansion of order 4 for couplings
between constraints inside triangles

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101

---

---

--- Thank You ---

---

---

There are: 480 Atoms

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
RMS relative constraint deviation after constraining: 1.20e-05
Initial temperature: 0.00193707 K

Started mdrun on rank 0 Mon Jul 27 19:37:07 2020

Step Time
0 0.00000

Constraint error in algorithm Lincs at step 0
Wrote pdb files with previous and current coordinates

Step 0 Warning: pressure scaling more than 1%, mu: 1.1089 1.1089 1.1089
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.75450e+02 3.14832e+02 1.63794e+06 0.00000e+00 1.63853e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
7.28303e+08 7.29942e+08 7.32011e+08 1.34039e+08 6.53415e+04
Constr. rmsd
1.05902e+01

Constraint error in algorithm Lincs at step 1
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 2
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 3
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 4
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 6
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 7
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 8
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 9
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 10
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 11
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 12
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 13
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 14
Wrote pdb files with previous and current coordinates

---

Program: gmx mdrun, version 2020.2
Source file: src/gromacs/mdlib/constr.cpp (line 224)

Fatal error:
Too many LINCS warnings (1046)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors

---

I am also having similar problem for month. I was trying to simulate tRNA and protein spontaneous binding using CG model. tRNA is modeled as " ss stiff" and the protein is modeled as elastic network. tRNA has total 493 beads and protein has 38 beads. Then I have placed the tRNA and protein CG model 7 angstroms apart in a cubic box of size 10.712 in all direction. Then I solvated it with 9167 W beads. As the system contains -72 net charge, I replace W beads with 200 WF beads and 72 NA beads in .top file and subtracted the same from W beads. During minimization using steepest descent method , system crashes after 3400 steps due to LINC warning. The main problem is occurring during equilibration and production runs. The system always crashes with the mentioned message:
Step 994945, time 19898.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms -nan, max 1921458.500000 (between atoms 508 and 509)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
494 496 91.7 192313.0000 62993.3828 0.3886
496 498 93.4 142471.3438 108772.3203 0.3900
498 501 116.7 236656.5000 52771.6914 0.3857
501 503 112.6 189481.7969 41774.4453 0.3926
503 506 85.6 217779.2031 85438.0859 0.3861
506 507 88.0 150803.8906 125992.8516 0.3876
507 511 90.4 65523.1250 206247.4219 0.3876
511 514 85.0 46650.6562 117849.0234 0.3892
514 515 91.3 111142.6953 165619.6562 0.3890
515 517 92.8 98818.0391 116848.1094 0.3876
517 521 93.9 143261.7344 114685.0547 0.3914
521 523 88.2 164716.5312 282818.2812 0.3827
523 525 103.2 394347.4062 121579.6328 0.3884
525 527 128.1 218091.1250 104837.9844 0.3857
527 528 103.6 178131.2344 103947.3984 0.3885
494 495 90.3 123926.3906 203927.0312 0.1900
501 502 93.4 102346.3594 160425.6406 0.1950
508 509 90.5 138798.7500 370841.6562 0.1930
508 510 89.6 82999.5547 248353.1250 0.2950
509 510 89.5 80491.1016 192618.2188 0.2160
515 516 91.3 157185.5469 227350.6562 0.1950
518 519 90.3 358042.7500 310516.5938 0.1930
518 520 90.3 391785.4062 292042.0625 0.2950
519 520 90.3 77126.2266 48872.2617 0.2160
521 522 88.8 278076.5625 113398.7891 0.1950
525 526 93.4 77316.5156 257994.0469 0.2500
529 530 90.3 114418.4844 137329.0312 0.1930
529 531 90.4 151761.8906 122067.7891 0.2950
530 531 90.6 103843.0234 57499.9727 0.2160
530 531 90.6 103843.0234 57499.9727 0.2160
Wrote pdb files with previous and current coordinates

Step 994946, time 19898.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms -nan, max 1323504.125000 (between atoms 515 and 516)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
494 496 89.9 62993.3828 200870.0000 0.3886
496 498 89.3 108772.3203 39699.6250 0.3900
498 501 87.7 52771.6914 189250.3750 0.3857
501 503 94.0 41774.4453 65956.5625 0.3926
503 506 89.8 85438.0859 191141.9375 0.3861
506 507 109.1 125992.8516 20439.9199 0.3876
507 511 91.3 206247.4219 174898.9219 0.3876
511 514 80.7 117849.0234 90270.7969 0.3892
514 515 103.6 165619.6562 253424.9844 0.3890
515 517 103.0 116848.1094 289925.9375 0.3876
517 521 102.5 114685.0547 196005.1875 0.3914
521 523 93.0 282818.2812 211365.5938 0.3827
523 525 92.0 121579.6328 177470.9688 0.3884
525 527 91.5 104837.9844 312076.5625 0.3857
527 528 85.7 103947.3984 123080.3516 0.3885
494 495 89.9 203927.0312 37546.2227 0.1900
501 502 89.6 160425.6406 173720.1875 0.1950
508 509 90.6 370841.6562 118846.5391 0.1930
508 510 90.9 248353.1250 68840.2656 0.2950
509 510 90.7 192618.2188 67430.7031 0.2160
515 516 103.0 227350.6562 258083.5000 0.1950
518 519 90.8 310516.5938 93413.1484 0.1930
518 520 90.5 292042.0625 114511.1953 0.2950
519 520 90.1 48872.2617 65457.5195 0.2160
521 522 92.0 113398.7891 135970.5469 0.1950
525 526 92.2 257994.0469 163851.6719 0.2500
529 530 90.1 137329.0312 127201.5234 0.1930
529 531 90.2 122067.7891 86580.9297 0.2950
530 531 90.1 57499.9727 101247.3281 0.2160
530 531 90.1 57499.9727 101247.3281 0.2160
Wrote pdb files with previous and current coordinates

Step 994947, time 19898.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms -nan, max 1812356.000000 (between atoms 508 and 509)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
494 496 88.9 200870.0000 40037.8047 0.3886
496 498 87.6 39699.6250 250771.5469 0.3900
498 501 127.3 189250.3750 86313.0234 0.3857
501 503 104.7 65956.5625 406241.1562 0.3926
503 506 134.9 191141.9375 60150.7500 0.3861
506 507 72.4 20439.9199 179357.0781 0.3876
507 511 86.9 174898.9219 85779.4922 0.3876
511 514 92.9 90270.7969 175175.6719 0.3892
514 515 90.6 253424.9844 282359.2500 0.3890
515 517 89.6 289925.9375 322200.2500 0.3876
517 521 124.6 196005.1875 393516.8125 0.3914
521 523 142.0 211365.5938 276678.6562 0.3827
523 525 87.3 177470.9688 220331.3125 0.3884
525 527 90.0 312076.5625 91688.6797 0.3857
527 528 91.3 123080.3516 125908.4375 0.3885
494 495 89.9 37546.2227 83503.8750 0.1900
501 502 105.6 173720.1875 190462.9688 0.1950
508 509 90.1 118846.5391 349784.8750 0.1930
508 510 90.1 68840.2656 204083.3438 0.2950
509 510 90.1 67430.7031 197279.6250 0.2160
515 516 89.7 258083.5000 171436.9688 0.1950
518 519 90.1 93413.1484 89503.9219 0.1930
518 520 90.1 114511.1953 66714.8984 0.2950
519 520 90.1 65457.5195 23229.5215 0.2160
521 522 145.9 135970.5469 275864.8750 0.1950
525 526 90.0 163851.6719 184313.4531 0.2500
529 530 90.1 127201.5234 228746.4688 0.1930
529 531 90.1 86580.9297 211168.5156 0.2950
530 531 90.3 101247.3281 82280.6562 0.2160
530 531 90.3 101247.3281 82280.6562 0.2160
Wrote pdb files with previous and current coordinates

Step 994948, time 19899 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms -nan, max 3874144.750000 (between atoms 521 and 522)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
494 496 82.7 40037.8047 90349.3984 0.3886
496 498 99.7 250771.5469 157688.9688 0.3900
498 501 138.7 86313.0234 202150.7031 0.3857
501 503 119.9 406241.1562 221955.6406 0.3926
503 506 108.1 60150.7500 341566.9688 0.3861
506 507 122.9 179357.0781 87361.4453 0.3876
507 511 101.7 85779.4922 187486.1562 0.3876
511 514 88.4 175175.6719 172085.6875 0.3892
514 515 153.4 282359.2500 72053.2109 0.3890
515 517 119.6 322200.2500 428320.2188 0.3876
517 521 166.4 393516.8125 770053.6875 0.3914
521 523 166.8 276678.6562 873867.0625 0.3827
523 525 143.4 220331.3125 572880.7500 0.3884
525 527 157.7 91688.6797 273149.5625 0.3857
527 528 104.7 125908.4375 154736.1406 0.3885
494 495 91.9 83503.8750 52442.6055 0.1900
501 502 113.1 190462.9688 211544.5781 0.1950
508 509 90.5 349784.8750 206982.3750 0.1930
508 510 90.0 204083.3438 188945.8594 0.2950
509 510 89.9 197279.6250 72651.3047 0.2160
515 516 86.3 171436.9688 203641.3750 0.1950
518 519 90.2 89503.9219 105677.3203 0.1930
518 520 90.0 66714.8984 137068.6094 0.2950
519 520 89.9 23229.5215 65879.9766 0.2160
521 522 158.4 275864.8750 755458.3750 0.1950
525 526 71.0 184313.4531 204919.8750 0.2500
529 530 90.4 228746.4688 115823.1641 0.1930
529 531 91.7 211168.5156 25196.6328 0.2950
530 531 90.2 82280.6562 95743.4766 0.2160
530 531 90.2 82280.6562 95743.4766 0.2160
Wrote pdb files with previous and current coordinates

Step 994949, time 19899 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms -nan, max 14196671.000000 (between atoms 521 and 522)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
494 496 90.1 90349.3984 209899.1875 0.3886
496 498 90.8 157688.9688 96980.5625 0.3900
498 501 106.4 202150.7031 145843.6250 0.3857
501 503 107.8 221955.6406 189348.5781 0.3926
503 506 120.2 341566.9688 82274.5391 0.3861
506 507 69.8 87361.4453 183451.2031 0.3876
507 511 80.6 187486.1562 266162.6250 0.3876
511 514 162.8 172085.6875 595004.0625 0.3892
514 515 164.7 72053.2109 1420512.8750 0.3890
515 517 173.4 428320.2188 2234810.0000 0.3876
521 523 169.9 873867.0625 3259775.0000 0.3827
523 525 154.5 572880.7500 2215942.5000 0.3884
525 527 165.1 273149.5625 1329909.8750 0.3857
527 528 80.0 154736.1406 548474.3750 0.3885
494 495 89.8 52442.6055 129903.7969 0.1900
501 502 113.9 211544.5781 111699.5938 0.1950
508 509 90.1 206982.3750 260962.8906 0.1930
508 510 90.4 188945.8594 77535.6406 0.2950
509 510 90.1 72651.3047 184413.6562 0.2160
515 516 143.4 203641.3750 1183828.0000 0.1950
518 519 89.8 105677.3203 281762.9062 0.1930
518 520 90.2 137068.6094 349846.3438 0.2950
519 520 89.8 65879.9766 164330.9844 0.2160
521 522 175.1 755458.3750 2768351.0000 0.1950
525 526 154.9 204919.8750 1383750.6250 0.2500
529 530 91.1 115823.1641 264650.7812 0.1930
529 531 89.1 25196.6328 263113.6875 0.2950
530 531 84.5 95743.4766 45084.3359 0.2160
530 531 84.5 95743.4766 45084.3359 0.2160
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

I have tried all the suggestion simillar to this topic on the forum but nothing worked. Help needed

I have tried Lincs-order=8,10,18,30 but nothing worked. Atomistic md is working fine with tRNA and protein. I have also coarse grained the RNA and protein model after energy minimization in all atom format. I have tried different tau_p values indicated in the forum, xtc-precision values, lincs-iter values etc. Nothing is working.

Time step of 0.01 didn't work but time step of 0.005 leads to 52 ns of production run before crashing.

Do you know if this is caused by RNA or the protein CG models? I would guess RNA.

I see you can run with 5 fs for a bit. If you re-start that simulation, can you go simulate further?

Nucleic acids Martini 2 models can't run with a time step >10 fs, as far as I know (e.g., recent work using 10 fs in production run), but you should be able to run with 10 fs with a properly setup system.