[gmx-users] Choosing LINCS setting / rcon for parallel mdrun

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Nov 16 02:09:22 CET 2015

Dear Users,

I tried to do a NVT run on a cluster with -np = 64. My system size is 12405
atoms ( a protein in water )

I get the following error.


There is no domain decomposition for 56 nodes that is compatible with the
given box and a minimum cell size of 0.959375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS

8 nodes were assigned for PME cal by mdrun

This is the part of my NVT.mdp

; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5         ; 10 fs
rlist       = 1.4      ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4      ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.12      ; grid spacing for FFT

I would still like to use 64 processes for the mdrun. Any suggestions

I am thinking of playing with -rcon. But I am not sure if it will affect
the accuracy of the simulation.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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