[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

[Mark Abraham]

http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the
ideas that will likely help you, e.g. smaller time step, more
equilibration-friendly pressure coupling.

Mark

On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

>
>
> It is 15 ns of NPT equilibration and I have not got a proper npt output
> yet to go to the MDrun. Because when I run the -mdrun command, I get fatal
> error as water molecule can not be settled.
>
> I guess that the system might need more equilibration.
>
> These are the settings of my npt.mdp file. The force field which I use is
> C36.
>
> integrator      = md            ; leap-frog integrator
> nsteps          =250000         ; 2 * 250000 = 500 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 1000           ; save coordinates every 0.2 ps
> nstvout         = 1000           ; save velocities every 0.2 ps
> nstenergy       = 1000           ; save energies every 0.2 ps
> nstlog          = 1000           ; update log file every 0.2 ps
>
> continuation    = yes            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-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           = 1.2           ; short-range neighborlist cutoff (in nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> vdwtype         = switch
> rvdw_switch     = 0.8
> ; 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          = Nose-Hoover     ; modified Berendsen thermostat
> tc-grps         = Protein POPC    SOL_CL    ; two coupling groups - more
> accurate
> tau_t           = 0.5   0.5   0.5    ; time constant, in ps
> ref_t           = 310   310   310  ; reference temperature, one for each
> group, in K
> pcoupl          = Parrinello-Rahman            ; no pressure coupling in
> NVT
> pcoupltype      = semiisotropic
> tau_p           = 4
> ref_p           = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
>
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = no    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no           ; assign velocities from Maxwell
> distribution
> ;gen_temp        = 310           ; temperature for Maxwell distribution
> ;gen_seed        = -1            ; generate a random seed
> nstcomm         = 1
> comm_mode       = Linear
> comm_grps       = Protein_POPC SOL_CL
>
> Would you please give me any sugestions? What are the possible problems
> might be considered?
>
>
> Thanks for your suggestions.
>
> Sincerely,
> Shima
>
>
> ________________________________
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, January 6, 2013 9:15 AM
> Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not
> the same as in Trajectory
>
>
>
> On 1/6/13 12:33 AM, Shima Arasteh wrote:
> > Do you mean that I re-run NPT step with the new index file and npt.gro
> (which I got from the last NPT equilibration)? That's not clear to me yet.
> >
>
> That's where I'd start.  You may have to run the new configuration through
> the entire equilibration protocol, though.  Instability during MD often
> indicates inadequate equilibration, so whatever your protocol is may not be
> sufficient as is and may require greater time.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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