# Minimization step does not move one

**URL:** <https://gromacs.bioexcel.eu/t/minimization-step-does-not-move-one/1008>\
**Category:** User discussions\
**Created:** [October 26, 2020, 4:47pm UTC](https://gromacs.bioexcel.eu/t/minimization-step-does-not-move-one/1008 "2020-10-26T16:47:01Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Nahuel08](https://avatars.discourse-cdn.com/v4/letter/n/ecb155/32.png) [@Nahuel08](https://gromacs.bioexcel.eu/u/Nahuel08)\
**Post date:** [October 26, 2020, 4:47pm UTC](https://gromacs.bioexcel.eu/t/minimization-step-does-not-move-one/1008/1 "2020-10-26T16:47:01Z")

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GROMACS version: 2018.1  
GROMACS modification: No

I have a membrane in all atom scale and with two phospholipids that i produce using CHARMM-GUI, after i download the gromacs files i make the README with the minimization, equilibration and production steps an executable and i run it.

I noticed a lot of linc warnings since the beginning but no error occured in the sense that my simulation seems to continue running, but it is not, is stucked in the minimization step, when i see the final lines in the log file says: Initializing Parallel LINear Constraint Solver and some quotes but nothing is happening i try modifying some aspects of the mdp file but nothing seems to work.

I dont know what to do. I know that lincs warning are an early warning that the system is unstable but it doesnt seem that way. When i visualize the membrane seems normal and changing nstxout = 1 does nothing because the minimization step is not running.

I hope i can get help, i been with this trouble for weeks and i really dont understand what the problem is. Thank you in advanced

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**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [October 26, 2020, 9:53pm UTC](https://gromacs.bioexcel.eu/t/minimization-step-does-not-move-one/1008/2 "2020-10-26T21:53:14Z")

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You will need to post what the actual messages are. Always provide more information than you think you need to. People you are asking to help can’t see what you see, don’t know what you know about what you are actually doing etc.

What is the command for the minimisation step? What is the output? Copy and paste the actual text.

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**Author:** ![Nahuel08](https://avatars.discourse-cdn.com/v4/letter/n/ecb155/32.png) [@Nahuel08](https://gromacs.bioexcel.eu/u/Nahuel08)\
**Post date:** [October 26, 2020, 10:22pm UTC](https://gromacs.bioexcel.eu/t/minimization-step-does-not-move-one/1008/3 "2020-10-26T22:22:34Z")

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**For the minimization step i use:**

gmx grompp -f step6.0\_minimization.mdp -o step6.0\_minimization.tpr -c step5\_input.gro -r step5\_input.gro -p topol.top  
gmx\_d mdrun -v -deffnm step6.0\_minimization

**The output until moment in the log file is:**

Linking all bonded interactions to atoms

Initiating Steepest Descents  
Atom distribution over 24 domains: av 12027 stddev 135 min 11856 max 12304  
Started Steepest Descents on rank 0 Mon Oct 26 10:58:11 2020

Steepest Descents:  
Tolerance (Fmax) = 1.00000e+03  
Number of steps = 5000

**but it stop in that step and does not continue with the minimization.**

 

**my mdp file is:**

define = -DPOSRES -DPOSRES\_FC\_BB=4000.0 -DPOSRES\_FC\_SC=2000.0 -DPOSRES\_FC\_LIPID=1000.0 -DDIHRES -DDIHRES\_FC=1000.0  
integrator = steep  
emtol = 1000.0  
nsteps = 5000  
nstlist = 10  
cutoff-scheme = Verlet  
rlist = 1.2  
vdwtype = Cut-off  
nstxout = 1  
vdw-modifier = Force-switch  
rvdw\_switch = 1.0  
rvdw = 1.2  
coulombtype = pme  
rcoulomb = 1.2  
lincs-order = 8  
lincs-iter = 2  
lincs\_warnangle = 45  
;  
constraints = h-bonds  
constraint\_algorithm = LINCS