# How to fix the LINCS warning problems during MD running that orignially obtained from Chamm-gui

**URL:** https://gromacs.bioexcel.eu/t/how-to-fix-the-lincs-warning-problems-during-md-running-that-orignially-obtained-from-chamm-gui/5185
**Category:** User discussions
**Tags:** forcefield, mdp-parameters, mdrun
**Created:** [November 6, 2022, 5:21am UTC](https://gromacs.bioexcel.eu/t/how-to-fix-the-lincs-warning-problems-during-md-running-that-orignially-obtained-from-chamm-gui/5185 "2022-11-06T05:21:25Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![Mark\_Chen](https://avatars.discourse-cdn.com/v4/letter/m/f0a364/32.png) [@Mark\_Chen](https://gromacs.bioexcel.eu/u/Mark_Chen)
#### Post date: [November 6, 2022, 5:21am UTC](https://gromacs.bioexcel.eu/t/how-to-fix-the-lincs-warning-problems-during-md-running-that-orignially-obtained-from-chamm-gui/5185/1 "2022-11-06T05:21:25Z")

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GROMACS version: 2022.1  
GROMACS modification: No

Dear Sir,  
I am a new one.  
I would like to ask a question. During running MD simulation, I got warning information.  
For example, I got the warning information: " Step 2496567, time 9986.27 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000196, max 0.003065 (between atoms 4041 and 4044) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4041 4043 31.5 0.1091 0.1088 0.1090 step 2496600, remaining wall clock time: 10 s

". Anyone could help me know how can I fix the LINCS WARNING？

Note, I prepared my MD simulation (ligand-protein complex) that got from CHARMM-GUI (Amber force field: ff19sb, OPC water model, gaff2, _hydrogen_ mass repartitioning (HMR))

## my md\_production.mdp:

integrator = md  
dt = 0.004  
nsteps = 2500000  
nstxtcout = 25000  
nstvout = 25000  
nstfout = 25000  
nstcalcenergy = 100  
nstenergy = 1000  
nstlog = 1000  
;  
cutoff-scheme = Verlet  
nstlist = 20  
vdwtype = Cut-off  
vdw-modifier = None  
DispCorr = EnerPres  
rvdw = 0.9  
rlist = 0.9  
rcoulomb = 0.9  
coulombtype = PME  
;  
tcoupl = V-rescale  
tc\_grps = SOLU SOLV  
tau\_t = 1.0 1.0  
ref\_t = 310 310  
;  
pcoupl = Parrinello-Rahman  
pcoupltype = isotropic  
tau\_p = 5.0  
compressibility = 4.5e-5  
ref\_p = 1.0  
;  
constraints = h-bonds  
constraint\_algorithm = LINCS  
continuation = yes  
;  
nstcomm = 100  
comm\_mode = linear  
comm\_grps = SOLU SOLV

Thank you very much

---

<div class="post-metadata">

### Author: ![miro\_astore](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/miro_astore/32/31_2.png) [@miro\_astore](https://gromacs.bioexcel.eu/u/miro_astore)
#### Post date: [December 30, 2022, 3:35pm UTC](https://gromacs.bioexcel.eu/t/how-to-fix-the-lincs-warning-problems-during-md-running-that-orignially-obtained-from-chamm-gui/5185/2 "2022-12-30T15:35:00Z")

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Hi. I’m having this issue as well (charmm forcefield) but only when I run the simulation over multiple nodes. I’m wondering if there is a bug or we need to use LINCS more carefully.

It helps if you can use constraints = all-bonds