[gmx-users] error while equilibration

[ananyachatterjee]

 I am trying to simulate RNA in water. I have minimized the system with 
 steepest Decent for 2000 steps and then with Conjugate gradient for till 
 the energy coverage reaches to 100 Kj/mol. But when I am trying to 
 equilibrate it I am getting following error

 -------------------------------------------------------
 Program mdrun, VERSION 4.5.5
 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 
 538

 Fatal error:
 11 particles communicated to PME node 3 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.
 For more information and tips for troubleshooting, please check the 
 GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 -------------------------------------------------------


 My nvt.mdp file contain

 title       = RNA complex NVT equilibration
 define      = -DPOSRES  ; position restrain
 ; 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
 energygrps  = RNA SOL NA
 ; 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 cells
 nstlist     = 5         ; 10 fs
 rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
 rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
 rvdw        = 1.4       ; 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
 tcoupl      = V-rescale                     ; modified Berendsen 
 thermostat
 tc-grps     = RNA SOL NA  ; two coupling groups - more accurate
 tau_t       = 0.1   0.1 0.1                     ; time constant, in ps
 ref_t       = 310   310 310                    ; reference temperature, 
 one for each group, in K
 ; Pressure coupling
 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    = 310       ; temperature for Maxwell distribution
 gen_seed    = -1        ; generate a random seed

 Please tell me where I am doing wrong.
 
-- 
 Ananya Chatterjee,
 Senior Research Fellow (SRF),
 Department of biological Science,
 IISER-Kolkata.