# Lincs warning during nvt equilibration

**URL:** <https://gromacs.bioexcel.eu/t/lincs-warning-during-nvt-equilibration/9666>\
**Category:** User discussions\
**Created:** [July 16, 2024, 9:29pm UTC](https://gromacs.bioexcel.eu/t/lincs-warning-during-nvt-equilibration/9666 "2024-07-16T21:29:54Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Somdatta](https://avatars.discourse-cdn.com/v4/letter/s/74df32/32.png) [@Somdatta](https://gromacs.bioexcel.eu/u/Somdatta)\
**Post date:** [July 16, 2024, 9:29pm UTC](https://gromacs.bioexcel.eu/t/lincs-warning-during-nvt-equilibration/9666/1 "2024-07-16T21:29:54Z")

</div>

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