# LINCS warning during energy minimization **URL:** \ **Category:** User discussions\ **Created:** [October 11, 2022, 9:13am UTC](https://gromacs.bioexcel.eu/t/lincs-warning-during-energy-minimization/4993 "2022-10-11T09:13:06Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![martina\_C](https://avatars.discourse-cdn.com/v4/letter/m/c67d28/32.png) [@martina\_C](https://gromacs.bioexcel.eu/u/martina_C)\ **Post date:** [October 11, 2022, 9:13am UTC](https://gromacs.bioexcel.eu/t/lincs-warning-during-energy-minimization/4993/1 "2022-10-11T09:13:06Z")
GROMACS version: 2022.3 GROMACS modification: No Hi everyone, I am running a simulation of a protein preparing the structure in CHARMM-GUI. I used the mdp file obtained by CHARMM-GUI but during the energy minimization it shows the following warning: Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 5000 Step= 0, Dmax= 1.0e-02 nm, Epot= 4.64660e+08 Fmax= 3.88728e+10, atom= 16241 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.11108e+08 Fmax= 1.33617e+10, atom= 16241 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.60567e+07 Fmax= 2.20310e+09, atom= 16241 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.29812e+06 Fmax= 2.52864e+08, atom= 16241 Step= 4, Dmax= 1.7e-02 nm, Epot= -1.39038e+06 Fmax= 2.01259e+07, atom= 4091 Step= 5, Dmax= 2.1e-02 nm, Epot= -1.87866e+06 Fmax= 2.62460e+06, atom= 16240 Step= 6, Dmax= 2.5e-02 nm, Epot= -1.95552e+06 Fmax= 5.41096e+05, atom= 16241 Step= 7, Dmax= 3.0e-02 nm, Epot= -1.97906e+06 Fmax= 1.31029e+05, atom= 16241 Step= 8, Dmax= 3.6e-02 nm, Epot= -1.98812e+06 Fmax= 5.19950e+04, atom= 16241 Step= 9, Dmax= 4.3e-02 nm, Epot= -1.99386e+06 Fmax= 1.89779e+04, atom= 16545 Step= 10, Dmax= 5.2e-02 nm, Epot= -2.00012e+06 Fmax= 1.27571e+05, atom= 16545 Step= 11, Dmax= 6.2e-02 nm, Epot= -2.00363e+06 Fmax= 1.13476e+04, atom= 16240 Step= 12, Dmax= 7.4e-02 nm, Epot= -2.00986e+06 Fmax= 9.47107e+04, atom= 16240 Step= 13, Dmax= 8.9e-02 nm, Epot= -2.01693e+06 Fmax= 5.51797e+04, atom= 16240 Step= 14, Dmax= 1.1e-01 nm, Epot= -2.01999e+06 Fmax= 4.25321e+04, atom= 16240 Step 15, time 0.015 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000016, max 0.000952 (between atoms 16243 and 16246) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 16227 16228 35.6 0.1090 0.1090 0.1090 Step= 16, Dmax= 6.4e-02 nm, Epot= -2.02320e+06 Fmax= 3.54836e+04, atom= 16240 Step= 17, Dmax= 7.7e-02 nm, Epot= -2.02465e+06 Fmax= 6.53873e+04, atom= 16240 Step= 18, Dmax= 9.2e-02 nm, Epot= -2.02726e+06 Fmax= 4.97583e+04, atom= 16240 Step= 20, Dmax= 5.5e-02 nm, Epot= -2.03076e+06 Fmax= 2.10320e+04, atom= 16240 Step= 21, Dmax= 6.7e-02 nm, Epot= -2.03132e+06 Fmax= 5.81503e+04, atom= 16240 Step= 22, Dmax= 8.0e-02 nm, Epot= -2.03454e+06 Fmax= 4.07968e+04, atom= 16240 Step= 24, Dmax= 4.8e-02 nm, Epot= -2.03758e+06 Fmax= 1.92212e+04, atom= 16240 Step= 26, Dmax= 2.9e-02 nm, Epot= -2.03906e+06 Fmax= 1.60387e+04, atom= 16240 Here is the mdp file I used: define = -DPOSRES -DPOSRES\_FC\_BB=400.0 -DPOSRES\_FC\_SC=40.0 integrator = steep emtol = 1000.0 nsteps = 5000 emstep = 0.01 nstlist = 10 cutoff-scheme = Verlet rlist = 0.9 vdwtype = Cut-off vdw-modifier = None DispCorr = EnerPres rvdw = 0.9 coulombtype = PME rcoulomb = 0.9 ; constraints = h-bonds constraint\_algorithm = LINCS Is this warning related to something wrong in my structure that I need to solve? Is it correct if I simply change the emstep to 0,005 (because I am quite new to gromacs and I have never found a value smaller than 0,01.) Otherwise I saw that I can avoid that lincs warning by changing the lincs-warnangle to 40 but I think this is a more important change than only changing the emstep. So, I was wondering which is the more correct way to solve the problem? Thank you very much ---
**Author:** ![ebriand](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ebriand/32/2314_2.png) [@ebriand](https://gromacs.bioexcel.eu/u/ebriand)\ **Post date:** [October 11, 2022, 12:04pm UTC](https://gromacs.bioexcel.eu/t/lincs-warning-during-energy-minimization/4993/2 "2022-10-11T12:04:33Z")
You can looks around the atoms implicated (circa 16240-16246 from the log) in your initial structure, and check for obvious problems in a visualization software. LINCS warnings are indeed indicative of a structure problem when they occur during a simulation. But seeing one or two during the first steps of energy minimization (as here) is not too worrying. Changing the emsteps would be okay, but possibly unecessary if that is the only LINCS warning. Changing the lincs-warnangle is inadvisable (masking rather than solving the problem). ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [October 14, 2022, 10:55am UTC](https://gromacs.bioexcel.eu/t/lincs-warning-during-energy-minimization/4993/3 "2022-10-14T10:55:48Z")
The CHARMM-GUI protocol also involves gradually releasing restraints, so in this case where several types of restraints are used simultaneously, they may be impeding progress toward the minimum. Subsequent minimizations with weaker (and ultimately no) restraints should complete smoothly. If not, there is something more fundamentally wrong with the system.