[gmx-users] MPI error in gromacs 4.6, more Errors

[Justin Lemkul]

On 3/24/14, 7:57 AM, Ankita Naithani wrote:
> Hi, so I modified my mdp file which now looks like the following:
>
> title        = production MD
> ; Run parameters
> integrator    = md        ; leap-frog algorithm
> ;nsteps        = 20000000    ; 0.005 * 20000000 = 100000 ps or 100 ns
> ;nsteps        = 200000    ; 0.005 * 200000 = 1 ns
> ;dt        = 0.005        ; 5 fs
> nsteps        = 33333333    ; 0.003 * 33333333 = 100000 ps or 100 n
> dt        = 0.003        ; 3 fs
> ; Output control
> nstxout        = 0        ; save coordinates every 2 ps
> nstvout        = 0        ; save velocities every 2 ps
> nstxtcout    = 1000        ; xtc compressed trajectory output every 5 ps
> nstenergy    = 1000            ; save energies every 5 ps
> nstlog        = 1000            ; update log file every 5 ps
> ; Bond parameters
> 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        = grid        ; search neighboring grid cells
> nstlist        = 5        ; 25 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)
> rlistlong    = 1.0        ; long-range neighborlist cutoff (in nm)
> cutoff-scheme   = Verlet
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order    = 4        ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> nstcomm = 10                    ; remove com every 10 steps
> ; 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        = 318     318    ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl          = berendsen    ; Berendsen thermostat
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 1.0        ; 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        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = yes        ; Velocity generation is on
> gen_temp    = 318        ; reference temperature, for protein in K
> --------------------------------------------------
>
>
> But, when I try to generate the tpr file on the cluster itself using
> gromacs 4.6.3, I get the following error:
>
>
> NOTE 1 [file md3.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
>
> NOTE 2 [file md3.mdp]:
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
>
> Generated 3403 of the 3403 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 3403 of the 3403 1-4 parameter combinations
> Segmentation fault
>
> Can anyone please suggest further?
>

Do as the notes suggest.  They're not fatal errors, they're just cautionary. 
You should probably educate yourself a bit further on what all of these 
algorithms are by taking a look at 
http://www.gromacs.org/Documentation/Cut-off_schemes.  The Verlet scheme is not 
mandatory, but it is required by the type of parallelization you requested.

Reviewers may question the changes in version and cutoff methods when critiquing 
your work, so be aware of that.  Also, the instability you are seeing is 
probably a result of the large time step, unless you are using virtual sites.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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