[gmx-users] Choosing LINCS setting / rcon for parallel mdrun
jalemkul at vt.edu
Mon Nov 16 02:14:40 CET 2015
On 11/15/15 8:09 PM, Agnivo Gosai wrote:
> 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
Your system is too small to decompose over 64 cores. One cannot arbitrarily
parallelize any system over any number of cores/nodes.
> 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.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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