GROMACS version: 2019
GROMACS modification: Yes/No
I am doing MD simulation of protein_DNA_ligand system and stopped at energy minimization step, I use gromacs 2019, forcefield AMBER99SB-ILDN, water model TIP3P.
After I do energy minimization for proten_DNA_ligand system with command:
gmx grompp -f em.mdp -maxwarn 1 -c rec_ion.gro -p top.top -o em.tpr
gmx mdrun -nt 12 -deffnm em -v
I visualized em.gro file by pymol it seems my protein structure is broken, is this ok?
blue: em.gro | green: rec_ion.gro
here is em.mdp file I set up. I would be grateful if you could point me to the problem I am having. Thank you very much
em.mdp
; Run control
integrator = steep
nsteps = 100000
; EM criteria and other stuff
emtol = 1000
emstep = 0.001
niter = 20
nbfgscorr = 10
; Output control
nstlog = 1
nstenergy = 1
; Neighborsearching and short-range nonbonded interactions
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
; Electrostatics
coulombtype = PME-switch
rcoulomb = 0.9
rcoulomb-switch = 0.88
cutoff-scheme=Verlet
vdw-modifier = Potential-shift
rvdw = 0.9
rvdw-switch = 0.88
epsilon-r = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
; Temperature and pressure coupling are off during EM
tcoupl = no
pcoupl = no
; Generate velocities to start
gen_vel = no
; options for bonds
constraints = none ; we only have C-H bonds here
; Type of constraint algorithm
continuation = no