[gmx-users] mpirun and no pbc

[Justin A. Lemkul]

shivangi nangia wrote:
> 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 error is telling you to use particle decomposition mode, i.e.:

mdrun -pd (other options...)

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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