# LINCS errors during NVT equilibration

**URL:** <https://gromacs.bioexcel.eu/t/lincs-errors-during-nvt-equilibration/848>\
**Category:** User discussions\
**Created:** [September 21, 2020, 7:23pm UTC](https://gromacs.bioexcel.eu/t/lincs-errors-during-nvt-equilibration/848 "2020-09-21T19:23:34Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Deniz](https://avatars.discourse-cdn.com/v4/letter/d/3da27b/32.png) [@Deniz](https://gromacs.bioexcel.eu/u/Deniz)\
**Post date:** [September 21, 2020, 7:23pm UTC](https://gromacs.bioexcel.eu/t/lincs-errors-during-nvt-equilibration/848/1 "2020-09-21T19:23:34Z")

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GROMACS version: 2019

Hi Gromacs users,

I am simulating a Ligand-Protein complex and I am getting the following LINCS errors while running the NVT equilibration;

_Step 129, time 0.258 (ps) LINCS WARNING_  
_relative constraint deviation after LINCS:_  
_rms 0.000005, max 0.000027 (between atoms 25756 and 25758)_  
_bonds that rotated more than 30 degrees:_

- atom 1 atom 2 angle previous, current, constraint length\*
- 8077 8078 46.6 0.1000 0.1000 0.1000\*

_Step 130, time 0.26 (ps) LINCS WARNING_  
_relative constraint deviation after LINCS:_  
_rms 0.000005, max 0.000018 (between atoms 23872 and 23873)_  
_bonds that rotated more than 30 degrees:_

- atom 1 atom 2 angle previous, current, constraint length\*
- 8077 8078 37.9 0.1000 0.1000 0.1000\*

_Step 131, time 0.262 (ps) LINCS WARNING_  
_relative constraint deviation after LINCS:_  
_rms 0.000005, max 0.000027 (between atoms 8213 and 8214)_  
_bonds that rotated more than 30 degrees:_

- atom 1 atom 2 angle previous, current, constraint length\*
- 8077 8078 31.2 0.1000 0.1000 0.1000\*

Fatal error:  
Too many LINCS warnings (1002)  
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.

**Please note that the errors are in the N-H bonds;**  
8077 (N) 8078 (H)  
25756 (NZ) and 25758 (HH11)  
23872 (NT) and 23873 (HD21)  
ARG: 8213 (NZ) and 8214 (HH11)

**The energy minimization converges :**  
Steepest Descents converged to Fmax \< 1000 in 2559 steps  
Potential Energy = -6.7342790e+06  
Maximum force = 9.9927802e+02 on atom 8041  
Norm of force = 1.0815428e+01

**My mdp file is:**  
title = NVT equilibration  
define = -DPOSRES ; position restrain the protein  
; Run parameters  
integrator = md ; leap-frog integrator  
nsteps = 50000 ; 2 \* 50000 = 100 ps  
dt = 0.002 ; 2 fs  
; Output control  
nstxout = 500 ; save coordinates every 1.0 ps  
nstvout = 500 ; save velocities every 1.0 ps  
nstenergy = 500 ; save energies every 1.0 ps  
nstlog = 500 ; update log file every 1.0 ps  
; Bond parameters  
continuation = no ; first dynamics run  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = h-bonds ; bonds involving H are constrained  
lincs\_iter = 1 ; accuracy of LINCS  
lincs\_order = 4 ; also related to accuracy  
; Nonbonded settings  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = grid ; search neighboring grid cells  
nstlist = 10 ; 20 fs, largely irrelevant with Verlet  
rlist = 1.4 ; short-range neighborlist cutoff (in nm)  
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)  
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)  
DispCorr = EnerPres ; account for cut-off vdW scheme  
; Electrostatics  
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.16 ; grid spacing for FFT  
; Temperature coupling is on  
tcoupl = V-rescale ; modified Berendsen thermostat  
tc-grps = Protein Non-Protein ; two coupling groups - more accurate  
tau\_t = 0.1 0.1 ; time constant, in ps  
ref\_t = 300 300 ; reference temperature, one for each group, in K  
; Pressure coupling is off  
pcoupl = no ; no pressure coupling in NVT  
; Periodic boundary conditions  
pbc = xyz ; 3-D PBC  
; Velocity generation  
gen\_vel = yes ; assign velocities from Maxwell distribution  
gen\_temp = 300 ; temperature for Maxwell distribution  
gen\_seed = -1 ; generate a random seed

I would appreciate any help.  
Deniz

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<div class="post-metadata">

**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [September 28, 2020, 8:19am UTC](https://gromacs.bioexcel.eu/t/lincs-errors-during-nvt-equilibration/848/2 "2020-09-28T08:19:15Z")

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Hi Deniz,

Note that this is a common issue ( see [https://gromacs.bioexcel.eu/search?q=lincs](https://gromacs.bioexcel.eu/search?q=lincs) )

Lincs warnings are usually pointing to an instability in the system; your system is not well enough equilibrated. There are a number of things you can do:

- decrease your simulation time step to 1fs for an additional equilibration
- use another thermostat for equilibration (v-rescale)
- use another barostat for equilibration (Berendsen for equilibration purposes only!)
- slowly warm up your system with simulated annealing
- manually inspect and fix the stereochemistry where the lincs warnings occur

You might find more suggestions in the search link above.