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

[Shima Arasteh]

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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