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

[Ankita Naithani]

Hi Justin,

Thank you very much for your reply. I shall try to work my way around and
see.


Kind regards,

Ankita


On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
Ankita Naithani