[gmx-users] Error while running free energy simulation.

[vivek sharma]

Dear Users,
I am trying to replicate the free energy tutorial by Dr Justin. In my
attempt I have calculated the OPLS-AA FF parameters for my molecules of
interest using acpype. I made the system in water and 1-octanol, While
running the independent lambda simulation for both the systems, I got an
error while running the simulation for 1-octanol system whereas the
simulation for water system were successful.

Following is the error message reported in failed simulation for 1-octanol
system
------------------------------------------------------------------
WARNING: Listed nonbonded interaction between particles 842 and 851
at distance 427.422 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

-----------------------------------------------------------------

I tried running the same system without free energy option ( free_energy
           = no), which was successful. It has narrowed the reason for
error to be the free energy code.
It will be really helpful if anybody can help me in understanding the
probable reason for error and any directions for handling this error.

Pasting below the mdp options for one of the independent lambda simulation
for reference.
-----------------------------------------------------------------------------------------------------------
; Run control
integrator               = sd       ; Langevin dynamics
tinit                    = 0
dt                       = 0.002
nsteps                   = 2500000   ; 5 ns
nstcomm                  = 100
; Output control
nstxout                  = 500
nstvout                  = 500
nstfout                  = 0
nstlog                   = 500
nstenergy                = 500
nstxout-compressed       = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme            = verlet
nstlist                  = 20
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2
; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.2
; van der Waals
vdwtype                  = cutoff
vdw-modifier             = potential-switch
rvdw-switch              = 1.0
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps                  = system
tau_t                    = 1.0
ref_t                    = 300
; Pressure coupling is on for NPT
Pcoupl                   = Parrinello-Rahman
tau_p                    = 1.0
compressibility          = 4.5e-05
ref_p                    = 1.0
; Free energy control stuff
free_energy              = yes
init_lambda_state        = 0
delta_lambda             = 0
calc_lambda_neighbors    = 1        ; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state        0    1    2    3    4    5    6    7    8    9
 10   11   12   13   14   15   16   17   18   19   20
vdw_lambdas              = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80
0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
coul_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00
; We are not transforming any bonded or restrained interactions
bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Not doing simulated temperting here
temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha                 = 0.5
sc-coul                  = no       ; linear interpolation of Coulomb (none
in this case)
sc-power                 = 1.0
sc-sigma                 = 0.3
couple-moltype           = FEL  ; name of moleculetype to decouple
couple-lambda0           = none      ; only van der Waals interactions
couple-lambda1           = vdw-q     ; turn off everything, in this case
only vdW
couple-intramol          = no
nstdhdl                  = 10
; Do not generate velocities
gen_vel                  = no
; options for bonds
constraints              = all-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation             = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 12
------------------------------------------------------------------------------------------------------------

Thanks in advance

regards,
Vivek Sharma