[gmx-users] MPI error in gromacs 4.6
Mark Abraham
mark.j.abraham at gmail.com
Mon Mar 24 13:25:28 CET 2014
No, semicolons start comments, not end lines
On Mar 24, 2014 1:07 PM, "Pavan Kumar" <kumar.pavan006 at gmail.com> wrote:
> It might be some typographical errors.
> Check the mdp file thoroughly. I think semicolon is required for the last
> line in your mdp file
>
>
> On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani
> <ankitanaithani at gmail.com>wrote:
>
> > 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > >
> > >
> > >
> > > --
> > > Cheers
> > > Pavan
> > > --
> > > Gromacs Users mailing list
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> >
> >
> >
> > --
> > Ankita Naithani
> > --
> > Gromacs Users mailing list
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>
>
>
> --
> Thanks & Regards,
> Pavan Kumar
> Project Engineer
> CDAC -KP
> Ph +91-7676367646
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