[gmx-users] MPI error in gromacs 4.6

[Pavan Kumar]

Hello Ankita
You have to just include the following line in your mdp file
cutoff-scheme=Verlet
And run your grompp with the modfied mdp file to generate tpr file and then
mdrun.
Hope this doesn't give you the same error


On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
<ankitanaithani at gmail.com>wrote:

> Hi,
>
> I am trying to run a simulation of my protein (monomer ~500 residues). I
> had few questions and erors regarding the same.
> I have previously run the simulation of the apo form of the same protein
> using Gromacs 4.5.5 which was available at the cluster facility I was using
> and also which is installed in my system. However, when I tried to run the
> holo form, I got error :
> Fatal error:
> 11 particles communicated to PME node 106 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> This I figured out could be solved using a lower timestep as my previous
> timestep was 4fs and now I have reduced it to 3fs which should work fine
> now.
> However, after producing the tpr file for production run in my GROMACS
> 4.5.5, I realised that the grant for the cluster facility is over and the
> new clusters which I am trying to set up the same protein for support only
> gromacs 4.6. I am trying to run the code in these clusters and I get he
> following error:
>
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.6.3
> Source code file: /home/gromacs-4.6.3/src/kernel/runner
> .c, line: 824
>
> Fatal error:
> OpenMP threads have been requested with cut-off scheme Group, but these are
> only
>  supported with cut-off scheme Verlet
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> ---------------------------------------------------------------------------------
>
> 1. I wanted help with my mdp options to make it compatible.
> 2. Since my pevious calculations were based on gromacs 4.5.5, switching to
> gromacs 4.6, would that break the continuity of the run or would that bring
> about differences in the way the trajectories would be analysed?
>
>
> Below, is my mdp file
> title        = production MD
> ; Run parameters
> integrator    = md        ; leap-frog algorithm
> 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
> energygrps      = Protein ATP
> ; 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)
> ; 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
>
>
>
>
> Kind regards--
> Ankita Naithani
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-- 
Cheers
Pavan