[gmx-users] REMD mdrun_mpi error

[Nawel Mele]

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          = 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