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