[gmx-users] Re: error during equilibriation

Sat Jun 11 13:45:20 CEST 2011

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.

On Sat, Jun 11, 2011 at 4:52 PM, Justin A. Lemkul <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>>
>> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110611/fe638f38/attachment.html>