[gmx-users] Periodic Molecule's Free Energy Calculation Error

Alex nedomacho at gmail.com
Wed Jul 12 04:52:40 CEST 2017


hBN is hardly a common subject of simulation for Gromacs folks, but 
let's see...

1. When you run the simulation in vacuum, do you get the same error? 
Does a 300K vacuum simulation result in reasonable sheet behavior? What 
about NVT?

2. What GROMACS forcefield are you using and what are the nonbonded 
types for boron and nitrogen?

3. How was the topology obtained? If x2top was used, was the BN sample 
in a box with in-plane PBC?

Alex


On 7/11/2017 8:39 PM, Jason Zhu wrote:
> Hello Gromacs Community,
>
> I am trying to calculate the solvation free energy of a hBN sheet following
> Justin Lemkul and Alchemistry's tutorials.
> Since the hBN sheet is infinitely large, I turned the periodic molecules
> flag on.
> This runs all fine on one core, but when I try to run NVT in parallel (e.g.
> 4 ranks), the job would throw the following error:
>
> A list of missing interactions:
>          LJC Pairs NB of 890400 missing 338688
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.4
> Source code file:
> /gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp,
> line: 242
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Halting parallel program gmx mdrun on rank 1 out of 4
> In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process
> 1)
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.4
> Source code file:
> /gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp,
> line: 242
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> It seems like a domain decomposition error. My first thought was that the
> system "explode".
> However, when I check my topology and pbc condition carefully, there is no
> sign of anything wrong.
> I also tried NPT & PROD MD. The same error when I ran on multiple MPI
> threads.
>
> My question is: why the system could run fine on one MPI, but not if I
> increased the number of MPI threads?
>
> Any help on this issue will be really appreciated.
>
>
> Here below is my .mdp file:
>
> ; RUN CONTROL—NVT
> ;——————————————————————————
> define       = -DPOSRES_HBN
> integrator   = sd            ; stochastic leap-frog integrator
> nsteps       = 5000          ; 2 * 5,000 fs = 10 ps
> dt           = 0.002         ; 2 fs
> comm-mode    = Linear        ; remove center of mass translation
> nstcomm      = 100           ; frequency for center of mass motion removal
>
> ;——————————————————————————
> ; OUTPUT CONTROL
> ;——————————————————————————
> nstxout                = 0          ; don't save coordinates to .trr
> nstvout                = 0          ; don't save velocities to .trr
> nstfout                = 0          ; don't save forces to .trr
> nstxout-compressed     = 5000       ; xtc compressed trajectory output
> every 5000 steps
> compressed-x-precision = 1000       ; precision with which to write to the
> compressed trajectory file
> nstlog                 = 5000       ; update log file every 10 ps
> nstenergy              = 5000       ; save energies every 10 ps
> nstcalcenergy          = 100        ; calculate energies every 100 steps
>
> ;——————————————————————————
> ; BONDS
> ;——————————————————————————
> constraint_algorithm   = lincs      ; holonomic constraints
> constraints            = all-bonds  ; hydrogens only are constrained
> lincs_iter             = 1          ; accuracy of LINCS (1 is default)
> lincs_order            = 4          ; also related to accuracy (4 is
> default)
> lincs-warnangle        = 30         ; maximum angle that a bond can rotate
> before LINCS will complain (30 is default)
> continuation           = no         ; formerly known as
> 'unconstrained-start' - useful for exact continuations and reruns
>
> ;——————————————————————————
> ; NEIGHBOR SEARCHING
> ;——————————————————————————
> cutoff-scheme   = Verlet
> ns-type         = grid   ; search neighboring grid cells
> nstlist         = 10     ; 20 fs (default is 10)
> rlist           = 1.2    ; short-range neighborlist cutoff (in nm)
> pbc             = xyz    ; 3D PBC
> ; PBC: grp is infinite
> periodic-molecules = yes
>
> ;——————————————————————————
> ; ELECTROSTATICS
> ;——————————————————————————
> coulombtype      = PME      ; Particle Mesh Ewald for long-range
> electrostatics
> rcoulomb         = 1.2      ; short-range electrostatic cutoff (in nm)
> ewald_geometry   = 3d       ; Ewald sum is performed in all three dimensions
> pme-order        = 4        ; interpolation order for PME (default is 4)
> fourierspacing   = 0.16     ; grid spacing for FFT
> ewald-rtol       = 1e-6     ; relative strength of the Ewald-shifted direct
> potential at rcoulomb
>
> ;——————————————————————————
> ; VDW
> ;——————————————————————————
> vdw-type                = PME
> rvdw                    = 1.2
> vdw-modifier            = Potential-Shift
> ewald-rtol-lj           = 1e-3
> lj-pme-comb-rule        = Geometric
> DispCorr                = EnerPres
>
> ;——————————————————————————
> ; TEMPERATURE & PRESSURE COUPL
> ;——————————————————————————
> tc_grps    =  System
> tau_t      =  0.1
> ref_t      =  300
> pcoupl     =  no
>
> ;——————————————————————————
> ; VELOCITY GENERATION
> ;——————————————————————————
> gen_vel      = yes       ; Velocity generation is on (if gen_vel is 'yes',
> continuation should be 'no')
> gen_seed     = -1       ; Use random seed
> gen_temp     = 300
>
> ;——————————————————————————
> ; FREE ENERGY CALCULATIONS
> ;——————————————————————————
> free-energy              = yes
> couple-moltype           = BNT
> couple-lambda0           = vdw-q
> couple-lambda1           = none
> couple-intramol          = no
> separate-dhdl-file       = yes
> sc-alpha                 = 0.5
> sc-power                 = 1
> sc-sigma = 0.3
> init-lambda-state        = 0
> coul-lambdas             = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0
> 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
> vdw-lambdas              = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5
> 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
> nstdhdl                  = 100
> calc-lambda-neighbors    = -1
>
>
> Best,
> Xuliang



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