GROMACS version:2019
GROMACS modification: Yes/No
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Hi Gromacs users,
I am simulating a Ligand-Protein complex and I am getting the following LINCS errors while running the NVT equilibration:
NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin threads to cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run multiple jobs).
Back Off! I just backed up nvt.edr to ./#nvt.edr.1#
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006886, max 0.199009 (between atoms 3927 and 3940)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004939, max 0.188633 (between atoms 3942 and 3944)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3940 3942 33.1 0.1530 0.1537 0.1335
starting mdrun ‘Protein in water’
100000 steps, 100.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004747, max 0.171485 (between atoms 3940 and 3942)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006200, max 0.284294 (between atoms 3940 and 3942)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3925 3927 31.8 0.1698 0.1709 0.1449
3927 3940 37.0 0.1825 0.1753 0.1522
3940 3942 42.7 0.1530 0.1715 0.1335
3942 3944 37.6 0.1735 0.1667 0.1449
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009708, max 0.235149 (between atoms 3925 and 3926)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.015093, max 0.319195 (between atoms 3925 and 3926)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3927 3940 32.2 0.1753 0.1178 0.1522
3940 3942 30.8 0.1715 0.1727 0.1335
3942 3943 39.2 0.1025 0.1078 0.1010
Step 2, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.062412, max 1.235228 (between atoms 3944 and 3962)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3910 3912 121.2 0.1184 0.0659 0.1449
3912 3913 108.1 0.0844 0.1085 0.1090
3912 3914 117.7 0.1170 0.0477 0.1526
3914 3916 33.3 0.1262 0.1918 0.1090
3917 3918 106.0 0.1071 0.0513 0.1090
3917 3919 114.2 0.1051 0.0378 0.1090
3917 3920 90.5 0.1466 0.0478 0.1522
3920 3921 37.5 0.1304 0.1882 0.1250
3923 3925 91.0 0.0946 0.0760 0.1335
3925 3926 104.1 0.0688 0.0462 0.1010
3927 3928 35.6 0.1278 0.0763 0.1090
3927 3940 84.3 0.1178 0.1196 0.1522
3929 3930 102.8 0.0959 0.0494 0.1090
3929 3931 109.7 0.0929 0.0432 0.1090
3929 3932 109.7 0.1296 0.0262 0.1526
3932 3933 33.4 0.1169 0.1627 0.1090
3940 3942 36.4 0.1727 0.2423 0.1335
3942 3943 73.0 0.1078 0.0392 0.1010
3942 3944 104.1 0.1197 0.0786 0.1449
3946 3947 120.5 0.0936 0.0596 0.1090
3946 3948 137.2 0.0948 0.0496 0.1090
3946 3949 151.6 0.1348 0.0378 0.1526
3949 3951 30.3 0.1188 0.1916 0.1090
3952 3954 45.1 0.1017 0.0560 0.1090
3955 3956 32.3 0.1139 0.1469 0.1090
3958 3960 31.0 0.1021 0.1008 0.1010
3962 3963 131.4 0.1046 0.0404 0.1229
3962 3964 123.4 0.1059 0.0515 0.1335
3966 3967 68.6 0.1029 0.0429 0.1090
3966 3982 165.6 0.1407 0.0264 0.1522
3982 3983 33.4 0.1281 0.1953 0.1229
Wrote pdb files with previous and current coordinates
This is my mdp file:
; Run control
integrator = sd ; Langevin dynamics
define = -DPOSRES
tinit = 0
dt = 0.001
nsteps = 100000 ; 100 ps
nstcomm = 10
nstcalcenergy = 10
; Output control
nstlog = 5000
; Neighborsearching and short-range nonbonded interactions
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
verlet-buffer-tolerance = 0.005
; Electrostatics
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 0.9
; van der Waals
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps = system
tau_t = 0.1
ref_t = 310
; Pressure coupling is off for NVT
Pcoupl = No
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; Generate velocities to start
gen_vel = yes
; options for bonds
constraints = all-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
ld_seed = -1
I would appreciate any help.
Nhina