[gmx-users] Re: error during equilibriation
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 11 13:47:57 CEST 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> sreelakshmi ramesh wrote:
>
>
>
> ---------- Forwarded message ----------
> From: *sreelakshmi ramesh* <sree.lakshmi at research.iiit.ac.in
> <mailto:sree.lakshmi at research.iiit.ac.in>
> <mailto: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> <mailto: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 <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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