Re: [gmx-users] REMD mdrun_mpi error
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/X/$TEMP/g
nvt.mdp nvt_$REP.mdp grompp -f nvt_$REP.mdp -c min.gro -p topol.top -o
eq_$REPBIS.tpr -maxwarn 1 rm -f tempdoneecho N REPLICAS = $nrepecho
Done.*
Nawel
2015-06-23 11:47 GMT+01:00 Mark Abraham mark.j.abra...@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.m...@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 :*
*title = CHARMM compound NVT equilibration define =
-DPOSRES ; position restrain the protein; Run
parametersintegrator = sd; leap-frog stochastic dynamics
integratornsteps = 100 ; 2 * 100 = 100
psdt = 0.002 ; 2 fs; Output controlnstxout =
500 ; save coordinates every 0.2 psnstvout =
10; 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 = 0.1 ; 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 = X X ; 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
Re: [gmx-users] REMD mdrun_mpi error
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.m...@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 :* *title = CHARMM compound NVT equilibration define = -DPOSRES ; position restrain the protein; Run parametersintegrator = sd; leap-frog stochastic dynamics integratornsteps = 100 ; 2 * 100 = 100 psdt = 0.002 ; 2 fs; Output controlnstxout = 500 ; save coordinates every 0.2 psnstvout = 10; 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 = 0.1 ; 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 = X X ; 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 10 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 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD mdrun_mpi error
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 :* *title = CHARMM compound NVT equilibration define = -DPOSRES ; position restrain the protein; Run parametersintegrator = sd; leap-frog stochastic dynamics integratornsteps = 100 ; 2 * 100 = 100 psdt = 0.002 ; 2 fs; Output controlnstxout = 500 ; save coordinates every 0.2 psnstvout = 10; 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 = 0.1 ; 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 = X X ; 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 10 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 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
