sreelakshmi ramesh wrote:
the same mdp file does the equlibriation fine at dt =0.0002 rather than
0.002.what could be the problem.if so can i continue using 0.0002 for dt
in this simulation.Anad also the cnt is not infinite adn also the
graphen sheets are not infinite.
Reducing the timestep can be effective when initial forces are too high and
cause everything to blow up. Decreasing it by 10x is usually not necessary and
suggests to me that you're dealing with a physically unreasonable system that
may or may not eventually blow up again.
I'd suspect that your EM was not sufficient, or your starting configuration is
not favorable, or perhaps both.
-Justin
On Sat, Jun 11, 2011 at 4:52 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
sreelakshmi ramesh wrote:
---------- Forwarded message ----------
From: *sreelakshmi ramesh* <[email protected]
<mailto:[email protected]>
<mailto:[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]> <mailto:[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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
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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