# Folding simulation output shows rotation and unfolding

**URL:** https://gromacs.bioexcel.eu/t/folding-simulation-output-shows-rotation-and-unfolding/7339
**Category:** User discussions
**Tags:** mdp-parameters, mdrun
**Created:** [October 6, 2023, 8:11am UTC](https://gromacs.bioexcel.eu/t/folding-simulation-output-shows-rotation-and-unfolding/7339 "2023-10-06T08:11:07Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![arijit93](https://avatars.discourse-cdn.com/v4/letter/a/c0e974/32.png) [@arijit93](https://gromacs.bioexcel.eu/u/arijit93)
#### Post date: [October 6, 2023, 8:11am UTC](https://gromacs.bioexcel.eu/t/folding-simulation-output-shows-rotation-and-unfolding/7339/1 "2023-10-06T08:11:08Z")

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GROMACS version:2022.4  
Hi,  
I am trying to do 10ns folding simulation for receptor terminals (N and C both). In the output, I observe the structure gets folded initially, but gradually after around 2.5-3ns, the structure starts to rotate and also unfolds in latter frames. Is this a normal occurrence, or 10ns simulation is too long?  
This is the mdp used for the simulation.  
title = Nk1R N-terminal domain folding simulation  
; Run parameters  
integrator = md ; leap-frog integrator  
;nsteps = 1000000 ; 0.002 \* 1000000 = 2 ns  
;nsteps = 250000 ; 0.002 \* 250000 = 0.5 ns  
nsteps = 5000000 ; 0.002 \* 5000000 = 10 ns  
dt = 0.002 ; 2 fs  
; Output control  
nstxout = 50 ; save coordinates every 0.1 ps  
nstvout = 1000 ; save velocities every 2 ps  
nstenergy = 1000 ; save energies every 2 ps  
nstlog = 1000 ; update log file every 2 ps  
; Bond parameters  
continuation = no ; not a restarted simulation  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained  
lincs\_iter = 1 ; accuracy of LINCS  
lincs\_order = 4 ; also related to accuracy  
; Neighborsearching  
cutoff-scheme = group  
ns\_type = grid ; search neighboring grid cels  
nstlist = 5 ; 10 fs  
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)  
; Implicit solvent  
implicit-solvent = GBSA  
gb-algorithm = Still  
rgbradii = 1.4  
; Electrostatics  
coulombtype = Cut-off ; Particle Mesh Ewald for long-range electrostatics  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.12 ; grid spacing for FFT  
; Temperature coupling is on  
tcoupl = v-rescale ; More accurate thermostat  
tc-grps = Protein ; one coupling group  
tau\_t = 0.1 ; time constant, in ps-1  
ref\_t = 310 ; reference temperature, one for each group, in K  
; Dispersion correction  
DispCorr = Ener ; account for cut-off vdW scheme  
; Velocity generation  
gen\_vel = no ; Velocity generation is off  
; COM motion removal  
; These options remove motion of the protein/bilayer relative to the solvent/ions  
nstcomm = 1  
comm-mode = Linear  
comm-grps = Protein  
; Scale COM of reference coordinates  
refcoord\_scaling = com

I also tried few by changing comm-mode from linear to angular, in which case the rotation and unfolding does not occur, but there is always a warning before the run about it being an artifact

WARNING 1 [file …/md\_gbsa\_2.mdp]:  
Removing the rotation around the center of mass in a periodic system,  
this can lead to artifacts. Only use this on a single (cluster of)  
molecules. This cluster should not cross periodic boundaries.

How should I approach these? Is the rotation and unfolding for 10ns folding simulation common, and if I should choose from the conformation before the rotation starts?  
Thank you in advance