GROMACS version: 2023.3
GROMACS modification: Yes/No
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Hi All,
I have created an implicit wall for this protein modeled from smog server in Z direction by implementing wall option in the .mdp file.However, with walls I have given the option for the pbc =xy. Need to run a coarse gain simulation with this system by using the following .mdp file .
; Run parameters
integrator = sd
nsteps = 100000000
dt = 0.0005
; Output control
nstxout = 10000 ; save coordinates every 1.0 ps
nstvout = 10000 ; save velocities every 1.0 ps
nstenergy = 10000 ; save energies every 1.0 ps
nstlog = 10000 ; update log file every 1.0 ps
xtc-grps = system ; save the whole system
energygrps = system ;group(s) to write to energy file
; Neighborsearching
ns_type=grid
nstlist = 20 ; 20 fs, largely irrelevant with Verlet scheme
rlist = 1.6 ;treatment of electrostatic interactions
rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm)
rvdw = 1.5 ; short-range van der Waals cutoff (in nm)
; Electrostatics
cutoff-scheme = verlet
coulombtype = Cut-off ;Make a grid in the box and only check atoms in neighboring grid cells
; Temperature coupling is on
tc-grps = system ; two coupling groups - more accurate
tau_t = 1.0 ; Temperature coupling time constant. Smaller values = stronger coupling
ref_t = 90.0 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no
; Periodic boundary conditions
pbc = xy
verlet-buffer-tolerance = -1
;walls
nwall = 1
wall-type = 9-3
wall-atomtype = X
wall-density = 100
wall-r-linpot = 1.00
; Set wall position explicitly (bottom only)
wall-ewald-zfac = 3
; Velocity generation
gen_vel = yes ; Velocity generation is on
gen_temp = 90.0
gen_seed = -1
ld_seed = -1
comm_mode = none ; center of mass velocity removal.
After running this script the following was the result.
With Verlet lists only full pbc or pbc=xy with walls is supported.
Can somebody tell how to get rid of this error?.