[gmx-users] MPI error in gromacs 4.6
Ankita Naithani
ankitanaithani at gmail.com
Mon Mar 24 12:48:23 CET 2014
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; 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
But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter
file.
On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar <kumar.pavan006 at gmail.com>wrote:
> 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
> --
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--
Ankita Naithani
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