search

tbereau / auto_martini

Automatic MARTINI parametrization of small organic molecules
GNU General Public License v2.0
59 stars 22 forks source link

LINCS warning #14

Open cherpradyumnsharma opened 6 years ago

cherpradyumnsharma commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 notifications@github.com 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 https://github.com/tbereau/auto_martini/issues/14#issuecomment-434239906, 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 commented 5 years ago

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