Lincs warning around C-H bond

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Dear all

I want to simulate a Poly phenylene oxide system. In time steps of 1 fs I face with lincs warning(atom C and H rotates more than 30 degree). I changes frames to 1 ps to see what happens for C-H bonds in CH# group. in VMD I saw CH3 group rotates abnormally and I think this the reason that I encounter with lincs warning. Althought, in time steps of 0.5 fs I do not recieve such warning. I drew structure on the paper here to show the problem better. what should I do for that? What is the main problem.

Thank you

Can you provide an image of what you mean by this? It will be much more diagnostic than a generic hand drawing of the structure.

If you’re getting instabilities even at δt = 1 fs, it suggests your topology is not stable and you should check and refine your parameters.

Thank you for your reply

I checked the parameters related to these atoms. It was correct and their parameters are very well known. is it possible any problem in mdp file?

All problem I have is related to these C-H bonds

I don’t see anything wrong with that geometry. Do you have a snapshot of a distorted geometry?

Without seeing the .mdp file, I have no idea. Please upload it or copy and paste its contents.

Dear Lemkuls

Thank you for your guidance. this is my .mdp file for NVT

;title = BTMA in water (Rezayani)
;define = -DDISRES (Nothing defined)

;disre = simple
;disre_weighting = conservative
;disre_fc = 10000

; Run parameters
integrator = md
nsteps = 5000000 ; 5 ns
dt = 0.001
; Output control
nstxout = 5000 ; save coordinates
nstvout = 5000 ; save velocities
nstenergy = 500 ; save energies
nstlog = 5000 ; update log file
nstxout-compressed = 500 ; xtc file

; Bond parameters
continuation = no
constraint_algorithm = lincs ; shake is another one
constraints = h-bonds ; all-bonds can be used too
lincs_iter = 1
lincs_order = 4

; Nonbonded settings
cutoff-scheme = Verlet
ns_type = grid
nstlist = 10
rcoulomb = 1.0
rvdw = 0.9
DispCorr = EnerPres

; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16

; Temperature coupling is on
tcoupl = nose-hoover
tc-grps = system
tau_t = 1
ref_t = 295 ; based on article temeprature

; Velocity generation
gen_vel = yes
gen_temp = 298
gen_seed = -1

; Periodic boundary conditions
pbc = xyz

Nothing looks unusual, so I would revisit the implementation of the force field parameters to make sure they are correct and reproduce some sensible target data, like a QM potential energy scan.

Dear Lemkul

I checked my .itp file . I found the problem. Some bonds were written two times. I removed and correct repetitive bonds and the problem were fixed.

Thank you