[gmx-users] mpirun and no pbc

[shivangi nangia]

Dear gmx-users,

I am heating my system at 300 K.

I have set the pbc conditions as "no"

I get the following error:
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 5436

Fatal error:
pbc type no is not supported with domain decomposition,
use particle decomposition: mdrun -pd
-------------------------------------------------------

I tried looking for a similar option as "-pd" for parallel runs, but could
not find any.

The md.mdp is:
; Run parameters
integrator  = md     ; leap-frog integrator
nsteps      = 500000 ; 2 * 500000 = 1000 ps, 1 ns
dt    = 0.002     ; 2 fs
; Output control
nstxout     = 1000      ; save coordinates every 2 ps
nstvout     = 1000      ; save velocities every 2 ps
nstxtcout   = 1000      ; xtc compressed trajectory output every 2 ps
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
; Bond parameters
continuation   = yes    ; Restarting after NPT
constraint_algorithm = lincs  ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1      ; accuracy of LINCS
lincs_order = 4      ; also related to accuracy
; Neighborsearching
ns_type     = simple      ; search neighboring grid cells
nstlist     = 5      ; 10 fs
rlist    = 1.0    ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw     = 1.0    ; short-range van der Waals cutoff (in nm)
; Electrostatics
;coulombtype = PME    ; Particle Mesh Ewald for long-range electrostatics
;pme_order   = 4      ; cubic interpolation
;fourierspacing = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale ; modified Berendsen thermostat
tc-grps     = Protein Non-Protein   ; two coupling groups - more accurate
tau_t    = 0.1 0.1   ; time constant, in ps
ref_t    = 400    400   ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl      = no
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p    = 2.0    ; time constant, in ps
ref_p    = 1.0    ; reference pressure, in bar
compressibility = 4.5e-5   ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc      = no    ; 3-D PBC
; Dispersion correction
DispCorr = no  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no     ; Velocity generation is off
;comm_mode
comm_mode = ANGULAR

Kindly guide regarding this.

Thanks,
SN
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