[gmx-users] Re: error during equilibriation

[sreelakshmi ramesh]

---------- Forwarded message ----------
From: sreelakshmi ramesh <sree.lakshmi at research.iiit.ac.in>
Date: Sat, Jun 11, 2011 at 4:37 PM
Subject: Re: error during equilibriation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


here goes my mdp file.The when i attach the top file by mail is
getting bounced back.Thanks in adcvance



title		= double walled cnt between graphene sheets
define		= -DPOSRES	; 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 cells
nstlist		= 5		; 10 fs
rlist		= 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)
; 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		= system	; two coupling groups - more accurate
tau_t		= 0.1		; time constant, in ps

ref_t		= 300 		; 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	= 300		; temperature for Maxwell distribution
gen_seed	= -1		; generate a random seed


here goes the error
Not all bonded interactions have been properly assigned to the domain
decomposition cells


A list of missing interactions:
               Angle of   2097 missing     14
      Ryckaert-Bell. of   1286 missing     12

               LJ-14 of   2801 missing      8
          exclusions of  31870 missing     14

Molecule type 'ICE'
the first 10 missing interactions, except for exclusions:
               LJ-14 atoms   79  299           global    79   299

               LJ-14 atoms  165  299           global   165   299
               Angle atoms  167  207  299      global   167   207   299
      Ryckaert-Bell. atoms  167  207  299  285 global   167   207   299   285

      Ryckaert-Bell. atoms  173  175  285  299 global   173   175   285   299
               LJ-14 atoms  173  299           global   173   299
               LJ-14 atoms  173  352           global   173   352
               Angle atoms  175  285  299      global   175   285   299

               Angle atoms  175  285  352      global   175   285   352
      Ryckaert-Bell. atoms  175  285  299  207 global   175   285   299   207

-------------------------------------------------------
Program mdrun, VERSION 4.5.3

Source code file: domdec_top.c, line: 356

Fatal error:
48 of the 46602 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body cut-off
distance (1 nm) or the two-body cut-off distance (1 nm), see option
-rdd, for pairs and tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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