[gmx-users] Re: error during equilibriation

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> 
> 
> ---------- Forwarded message ----------
> From: *sreelakshmi ramesh* <sree.lakshmi at research.iiit.ac.in 
> <mailto: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 
> <mailto: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

Is the CNT and/or the graphene infinite?  If any species are, then you need to 
use the periodic_molecules keyword.

How successful was energy minimization?  What was the output (Fmax and Epot)?

I see nothing particularly wrong with the .mdp file (other than perhaps the 
keyword mentioned above), so that suggests either the topology or the initial 
configuration is not sound.

-Justin

> 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
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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