Lincs warning

GROMACS version: 2020.1
GROMACS modification: No
Hello everyone,

I have been trying to simulate a protein in water, but the following error appears:

Fatal error:

Too many LINCS warnings (1436)

If you know what you are doing you can adjust the warning threshold links in your MDP file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem

I already simulated the protein in vacuo and as a complex, the simulation went normally.

However, when I try to simulate only the protein in water the production doesn’t start.

I am using an HPC to run the simulation. I use 2 GPUs and 8 Threads. I noticed that the problem doesn’t appear when I don’t use the GPU but the calculation takes a long time and becomes unfeasible.

I forward the .sh file

#!/bin/bash -v

#SBATCH --partition=GPUSP4

#SBATCH --ntasks=2 # number of tasks / mpi processes

#SBATCH --cpus-per-task=8 # Number OpenMP Threads per process


#SBATCH --time=80:00:00

#SBATCH --gres=gpu:tesla:2

#OpenMP settings:



export OMP_PLACES=threads

export OMP_PROC_BIND=spread

echo $SLURM_JOB_ID #ID of job allocation

echo $SLURM_SUBMIT_DIR #Directory job where was submitted

echo $SLURM_JOB_NODELIST #File containing allocated hostnames

echo $SLURM_NTASKS #Total number of cores for job

module load Gromacs/2019.3-cuda

#run the application:

gmx mdrun -pin on -ntmpi 2 -ntomp 8 -deffnm md -v