sreelakshmi ramesh wrote:
---------- Forwarded message ----------
From: *sreelakshmi ramesh* <[email protected]
<mailto:[email protected]>>
Date: Sat, Jun 11, 2011 at 4:37 PM
Subject: Re: error during equilibriation
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
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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