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[Dr. Vitaly Chaban]

This usually means that your system is not well equilibrated.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 15, 2014 at 6:13 AM, Padmani Sandhu
<padmanisandhu09 at gmail.com> wrote:
> Hello,
>
>
> I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
> in POPC lipid membrane. After energy minimizing of complex, I am facing
> problem with NVT equilibration step. mdrun crashed with following error:
>
>
> "12 particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated."
>
>
>
>
> These are the parameters used in nvt.mdp file:
>
> title           = NVT equilibration
>
> define          = -DPOSRES_LIPID -DPOSRES
> -DPOSRES_WATER  ; position restrain the protein
>
> ; Run parameters
>
> integrator      = md            ; leap-frog integrator
>
> nsteps          = 50000         ; 2 * 50000 = 100 ps
>
> dt                  = 0.002             ; 2 fs
>
> ; Output control
>
> nstxout         = 100           ; save coordinates every 0.2 ps
>
> nstvout         = 100           ; save velocities every 0.2 ps
>
> nstenergy       = 100           ; save energies every 0.2 ps
>
> nstlog          = 100           ; update log file every 0.2 ps
>
> ; Bond parameters
>
> continuation    = no                ; first dynamics run
>
> 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 cels
>
> nstlist         = 5                 ; 10 fs
>
> rlist           = 1.2           ; short-range neighborlist cutoff
> (in nm)
>
> rcoulomb        = 1.2           ; short-range electrostatic
> cutoff (in nm)
>
> rvdw            = 1.2           ; short-range van der Waals 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
>
> ; Temperature coupling is on
>
> tcoupl          = V-rescale                 ; modified
> Berendsen thermostat
>
> tc-grps         = Protein_LMT POPC Water_and_ions       ;
> three coupling groups - more accurate
>
> tau_t           = 0.1   0.1     0.1             ; time constant, in
> ps
>
> ref_t           = 271   271     271             ; reference
> temperature, one for each group, in K
>
> ; Pressure coupling is off
>
> pcoupl          = no            ; no pressure coupling in NVT
>
> ; Periodic boundary conditions
>
> pbc                 = xyz               ; 3-D PBC
>
> ; Dispersion correction
>
> DispCorr        = EnerPres      ; account for cut-off vdW
> scheme
>
> ; Velocity generation
>
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
>
> gen_temp        = 271           ; temperature for Maxwell
> distribution
>
> gen_seed        = -1            ; generate a random seed
>
> ; COM motion removal
>
> ; These options remove motion of the
> protein/bilayer relative to the solvent/ions
>
> nstcomm         = 1
>
> comm-mode       = Linear
>
> comm-grps       = Protein_LMT_POPC Water_and_ions
>
>
>
>
> Please help me...!!!!
>
>
>
>
> --
> *Padmani sandhu*
> *Research Scholar,*
> *Center for Computational Biology and Bioinformatics,*
> *Central University of Himachal Pradesh,*
> *Temporary Academic Block, Shahpur *
> *Pin 176206, District Kangra,*
> *Himachal Pradesh, India*
> --
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