LINCS warning

[cherpradyumnsharma]

Hi
I used your script to get parameters for some small molecules. But when i run these simulations on gromacs I get lot of LINCS warning for these simulations for timestep greater than 10 femtoseconds. Something like

##############################################
Step 40342, time 806.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003365, max 0.006212 (between atoms 2 and 5)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 31.0 0.2399 0.2399 0.2400

#################################################
My mdp file

integrator = md
tinit = 0.0
dt = 0.02
nsteps = 500000

nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 303.15

; Pressure coupling:
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 12
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no

refcoord_scaling = all

[tbereau]

Hard to tell without information about the molecule and its CG representation, but I guess it's due to intramolecular interactions. Check if you have lots of rings, creating lots of constraints. In that case you may want to replace some of them with virtual sites. Otherwise look out for too many dihedrals in the molecule (maybe some redundancies?).

[cherpradyumnsharma]

Hi I am attaching the sdf files of molecules and also the itp and gro files I got using your script.

…

On Tue, Oct 30, 2018 at 3:31 PM Tristan Bereau ***@***.***> wrote: Hard to tell without information about the molecule and its CG representation, but I guess it's due to intramolecular interactions. Check if you have lots of rings, creating lots of constraints. In that case you may want to replace some of them with virtual sites. Otherwise look out for too many dihedrals in the molecule (maybe some redundancies?). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AqaVnFB_IIhe5j6aKbMZK663B8jJDTEcks5uqCOPgaJpZM4X6XzS> .

-- Regards Pradyumn Sharma PhD Student Department of Chemical Engineering Indian Institute Of Science (IISc)

[tbereau]

See my last message, hopefully this gives you some clues to fix the force field.