[gmx-users] Simulation Crash

[Udaya Dahal]

​​I have a polymer and water simulation. Since I am using the buckingham
and the LJ potential, I am using the table for the non bonded pairwise
interaction. The system blows up. Since the starting configuration matters
a most for the simulation, I used packmol to generate the starting
structure and run energy minimization. I tested the rdf of the system and
it shows that there is no atom close by confirming that there is no
overlap(except for 0.015nm which is for virtual site I guess for tip4p
water model I am using).

the eq.mdp file is attached here.

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include                  =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define                   =

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0.0
dt                       = 0.00001
nsteps                   = 5000000
; For exact run continuation or redoing part of a run
init-step                = 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation-part          = 1
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = system

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld-seed                  = 1993

energygrps               = C2 C3 OP HP H IW OWT4

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (group: using charge groups, Verlet: particle based
cut-offs)
cutoff-scheme            = group
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic-molecules       = no
; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-drift      = 0.005
; nblist cut-off
rlist                    = 1
; long-rang​
 files_simulation_polymer_water.tar
<https://docs.google.com/file/d/0ByXdaXpbCwOyckFhTFNqdDhYWWs/edit?usp=drive_web>
​e cut-off for switched potentials
rlistlong                = -1
nstcalclr                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME-User
coulomb-modifier         = Potential-shift-Verlet
rcoulomb_switch          = 0.0
rcoulomb                 = 0.8
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 40
epsilon-rf               = 0
; Method for doing Van der Waals
vdw_type                 = User
vdw-modifier             = Potential-shift-Verlet
; cut-off lengths
rvdw_switch              = 0.9
rvdw                     = 0.8
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Separate tables between energy group pairs
energygrp_table          = C2 C2 C2 H C2 HP C2 IW C2 OP C2 OWT4 C3 C2 C3 C3
C3 H C3 HP C3 IW C3 OP C3 OWT4 H H H IW HP H HP HP HP IW HP OP HP OWT4 IW
IW OP H OP HP OP IW OP OP OP OWT4 OWT4 H OWT4 IW OWT4 OWT4
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
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
optimize-fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl                   = v-rescale
nsttcouple               = -1
nh-chain-length          = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps                  = system
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 298
; pressure coupling
Pcoupl                   = berendsen
Pcoupltype               = isotropic
nstpcouple               = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1
; Scaling of reference coordinates, No, All or COM
refcoord-scaling         = All

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
gen_temp                 = 298
gen_seed                 = 473529

; OPTIONS FOR BONDS
constraints              = all-bonds
; Type of constraint algorithm
constraint_algorithm     = Lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs_order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs_warnangle          = 30
; Convert harmonic bonds to morse potentials
morse                    = no

In case if you need the files i am simulating i have attached the files in
the google drive as well.
https://drive.google.com/file/d/0ByXdaXpbCwOyckFhTFNqdDhYWWs/view?usp=sharing

Thanks,
Udaya