GROMACS version: 2024.2
GROMACS modification: Yes/No
Hi I am running a CG simulation (MARTINI2.0), during NVT equilibration with position restraint.
I received couple of LINCS WARNING.the error i am attaching here
GROMACS - gmx mdrun, 2022.5-plumed_2.8.3 (-:
Executable: /home/adlab/apps/conda/gromacs-2022.5/build/bin/gmx_mpi
Data prefix: /home/adlab/apps/conda/gromacs-2022.5 (source tree)
Working dir: /home/adlab/somdatta_martiniTutorial/martini_setup/NVT_RUN
Command line:
gmx_mpi mdrun -s nvt-eq-t1.tpr -v -deffnm nvt-eq-t1
Back Off! I just backed up nvt-eq-t1.log to ./#nvt-eq-t1.log.1#
Reading file nvt-eq-t1.tpr, VERSION 2022.5-plumed_2.8.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1.4 to 1.549
Using 8 MPI processes
Using 6 OpenMP threads per MPI process
Back Off! I just backed up nvt-eq-t1.xtc to ./#nvt-eq-t1.xtc.1#
Back Off! I just backed up nvt-eq-t1.edr to ./#nvt-eq-t1.edr.1#
starting mdrun ‘Protein in INSANE! Membrane UpperLeaflet>POPC:PAPC:PNGS:PAPE:DPSM:CHOL=45.0:15.0:29.0:24.0:26.0:113.0 LowerLeaflet>POPC:PAPC:PAPE:DPSM:PAPS:PAP6:CHOL=35.0:2.0:52.0:5.0:37.0:3.0:109.0’
5000 steps, 50.0 ps.
step 0
step 100, remaining wall clock time: 109 s
vol 0.85 imb F 149% step 200, remaining wall clock time: 123 s
step 300, remaining wall clock time: 123 s
vol 0.49 imb F 94% step 400, remaining wall clock time: 124 s
step 500, remaining wall clock time: 116 s
Step 597, time 5.97 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000437, max 0.009129 (between atoms 373 and 378)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
380 382 33.7 0.3100 0.3116 0.3100
378 380 30.3 0.3100 0.3112 0.3100
vol 0.41! imb F 53%
Step 600, time 6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.040245, max 20.810877 (between atoms 373 and 378)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
380 382 87.6 0.3098 3.3782 0.3100
382 383 90.8 0.3106 5.1112 0.3100
387 391 55.8 0.3100 0.4374 0.3100
383 387 89.5 0.3108 2.5769 0.3100
373 378 63.5 0.3302 7.1976 0.3300
378 380 128.8 0.3074 5.9510 0.3100
Wrote pdb files with previous and current coordinates
step 600, remaining wall clock time: 119 s
Step 601, time 6.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 2.076999, max 38.945858 (between atoms 378 and 380)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
380 382 74.1 3.3782 12.1198 0.3100
382 383 84.7 5.1112 10.6351 0.3100
391 394 57.3 0.3302 0.4168 0.3100
387 391 90.0 0.4374 2.7449 0.3100
384 385 49.4 0.2700 0.2854 0.2700
384 386 44.6 0.2700 0.2600 0.2700
383 387 90.0 2.5769 3.3764 0.3100
373 378 90.0 7.1976 6.6792 0.3300
378 380 110.9 5.9510 12.3832 0.3100
Wrote pdb files with previous and current coordinates
I energy minimized the system which is showing
Steepest Descents converged to machine precision in 5971 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -8.5996931e+05
Maximum force = 3.5251316e+03 on atom 380
Norm of force = 3.4515096e+01
that means that the energy is minimized but I cnat understand why everytime its showing LINCS warning. I increase the emsteps then tried NVT to run with that tpr but every time its showing several LINCS warning … I tried to run the NVT equilibration for 50ps . I am attaching the minimization.mdp and .mdp of nvt and the command I am using is also attached
gmx_mpi grompp -f minimization.mdp -c system_ions.gro -p topol.top -o em2.tpr
gmx_mpi mdrun -deffnm em2 -v
gmx_mpi grompp -f martini_nvt.mdp -c em2.gro -r em2.gro -n system.ndx -p topol.top -o nvt-eq-t1.tpr
mpirun -np 8 gmx_mpi mdrun -s nvt-eq-t1.tpr -v -deffnm nvt-eq-t1
nvt.mdp
define = -DPOSRES
integrator = md
dt = 0.01
nsteps =5000 ;= 50ps
nstcomm = 100
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 2000 ; Output frequency for energies to log file
nstenergy = 200 ; Output frequency for energies to energy file
nstxtcout = 2000 ; Output frequency for .xtc file
xtc_precision = 200
;energygrps = lipids W_ION
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = cut-off ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.4
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.4 ;1.1 (for use with Verlet-pairlist)
;cutoff-scheme = verlet
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
tcoupl = V-rescale
tc-grps = PROTEIN LIGAND MEMB SOLV
tau_t = 1.0 1.0 1.0 1.0
ref_t = 299 299 299 299
Pcoupl = no ;berendsen ; parrinello-rahman ; parrinello-rahman
gen_vel = yes
gen_temp = 299
gen_seed = 473529
; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
minimization.mdp
Define = -DFLEXIBLE
integrator = steep
dt = 0.002
nsteps = 100000
nstcomm = 100
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
coulombtype = reaction-field
rcoulomb = 1.4
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.4
I am applying position restraint only in the Protein in my system in equilibration step