[gmx-users] REMD mdrun_mpi error
Nawel Mele
nawel.mele at gmail.com
Tue Jun 23 17:03:23 CEST 2015
Hi Mark,
I tried to run an individual tpr file and it crashed:
Double sids (0, 1) for atom 26
Double sids (0, 1) for atom 27
Double sids (0, 1) for atom 28
Double sids (0, 1) for atom 29
Double sids (0, 1) for atom 30
Double sids (0, 1) for atom 31
Double sids (0, 1) for atom 32
Double sids (0, 1) for atom 33
Double sids (0, 1) for atom 34
Double sids (0, 1) for atom 35
Double sids (0, 1) for atom 36
Double sids (0, 1) for atom 37
Double sids (0, 1) for atom 38
Double sids (0, 1) for atom 39
Double sids (0, 1) for atom 40
-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file:
/local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c,
line: 99
Fatal error:
Double entries in block structure. Item 53 is in blocks 1 and 0
Cannot make an unambiguous inverse block.
To create my tpr files I useda bash script like this:
*#!/bin/bash -fnrep=`wc temperatures.dat | awk '{print $1}'`echo
$nrepcount=0count2=-1for TEMP in `cat temperatures.dat`do let count2+=1
REP=`printf "%03d" $count2` REPBIS=`printf "%d" $count2` echo
"TEMPERATURE: $TEMP K ==> FILE: nvt_$REP.mdp" sed "s/XXXXX/$TEMP/g"
nvt.mdp > nvt_$REP.mdp grompp -f nvt_$REP.mdp -c min.gro -p topol.top -o
eq_$REPBIS.tpr -maxwarn 1 rm -f tempdoneecho "N REPLICAS = $nrep"echo "
Done."*
Nawel
2015-06-23 11:47 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> Hi,
>
> Do your individual replica .tpr files run correctly on their own?
>
> Mark
>
> On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele <nawel.mele at gmail.com> wrote:
>
> > Dear gromacs users,
> >
> > I am trying to simulate a ligand using REMD method in explicit solvent
> with
> > the charmm force field. When I try to equilibrate my system I get this
> > error :
> >
> > Double sids (0, 1) for atom 26
> > Double sids (0, 1) for atom 27
> > Double sids (0, 1) for atom 28
> > Double sids (0, 1) for atom 29
> > Double sids (0, 1) for atom 30
> > Double sids (0, 1) for atom 31
> > Double sids (0, 1) for atom 32
> > Double sids (0, 1) for atom 33
> > Double sids (0, 1) for atom 34
> > Double sids (0, 1) for atom 35
> > Double sids (0, 1) for atom 36
> > Double sids (0, 1) for atom 37
> > Double sids (0, 1) for atom 38
> > Double sids (0, 1) for atom 39
> > Double sids (0, 1) for atom 40
> >
> > -------------------------------------------------------
> > Program mdrun_mpi, VERSION 4.6.5
> > Source code file:
> > /local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c,
> > line: 99
> >
> > Fatal error:
> > Double entries in block structure. Item 53 is in blocks 1 and 0
> > Cannot make an unambiguous inverse block.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> >
> > *My mdp input file looks like this :*
> >
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> >
> > *title = CHARMM compound NVT equilibration define =
> > -DPOSRES ; position restrain the protein; Run
> > parametersintegrator = sd ; leap-frog stochastic dynamics
> > integratornsteps = 1000000 ; 2 * 1000000 = 100
> > psdt = 0.002 ; 2 fs; Output controlnstxout =
> > 500 ; save coordinates every 0.2 psnstvout =
> > 100000 ; save velocities every 0.2 psnstenergy = 500
> > ; save energies every 0.2 psnstlog = 500 ; update log
> > file every 0.2 ps; Bond parameterscontinuation = no ; first
> > dynamics runconstraint_algorithm = SHAKE ; holonomic constraints
> > constraints = h-bonds ; all bonds (even heavy atom-H bonds)
> > constrainedshake-tol = 0.00001 ; relative tolerance for
> SHAKE;
> > Neighborsearchingns_type = grid ; search neighboring
> grid
> > cellsnstlist = 5 ; 10 fsrlist = 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); Electrostaticscoulombtype =
> > PME ; Particle Mesh Ewald for long-range
> > electrostaticspme_order = 4 ; Interpolation order for
> > PME. 4 equals cubic interpolationfourierspacing = 0.16 ; grid
> > spacing for FFT; Temperature coupling is on;tcoupl = V-rescale
> > ; modified Berendsen thermostattc-grps = LIG SOL ; two
> > coupling groups - more accuratetau_t = 1.0 1.0 ; time
> > constant, in psref_t = XXXXX XXXXX ; reference
> > temperature, one for each group, in K;Langevin dynamicsbd-fric =
> 0
> > ; ;Brownian dynamics friction coefficient. ld-seed
> > =-1; ;pseudo random seed is used; Pressure coupling is
> > offpcoupl = no ; no pressure coupling in NVT;
> Periodic
> > boundary conditionspbc = xyz ; 3-D PBC; Dispersion
> > correctionDispCorr = EnerPres ; account for cut-off vdW
> scheme;
> > Velocity generationgen_vel = yes ; assign velocities
> from
> > Maxwell distributiongen_temp = 0.0 ; temperature for
> > Maxwell distributiongen_seed = -1 ; generate a random
> > seed*
> >
> >
> > *And my input file to run it in parallel looks like that:*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *#!/bin/bash#PBS -l nodes=3:ppn=16#PBS -l walltime=00:10:00#PBS -o
> > zzz.qsub.out#PBS -e zzz.qsub.errmodule load openmpi module load
> > gromacs/4.6.5mpirun -np 48 mdrun_mpi -s eq_.tpr -multi 48 -replex 100000
> > >& faillog-X.log*
> >
> >
> > Does anyone have seen this issue before??
> >
> > Many thanks,
> > --
> >
> > Nawel Mele, PhD Research Student
> >
> > Jonathan Essex Group, School of Chemistry
> >
> > University of Southampton, Highfield
> >
> > Southampton, SO17 1BJ
> > --
> > Gromacs Users mailing list
> >
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> >
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--
Nawel Mele, PhD Research Student
Jonathan Essex Group, School of Chemistry
University of Southampton, Highfield
Southampton, SO17 1BJ
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