[gmx-users] NPT Equilibration error

[Justin Lemkul]

On 8/22/12 8:26 AM, Ankita naithani wrote:
> Hi,
>
> I am trying to run NPT equilibration on two separate systems both with
> ligands present in the structure.
>
> However, I got two different errors for both of these and these are below:
>
> Fatal error: A charge group moved too far between two domain
> decomposition steps.
>
> Fatal error: 8 particles communicated to PME node 1 are more than 2/3
> times the cut off out of the domain decomposition cell of their charge
> group in dimension X.
>

In general, both errors mean your system is blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

> My npt.mdp files looks like follows:
>
> title           = NPT equilibration
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 125000        ; 250 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 0             ; save coordinates every 5 ps
> nstvout         = 0             ; save velocities every 5 ps
> nstenergy       = 10            ; save energies every 5 ps
> nstlog          = 1000          ; update log file every 5 ps
> ; Bond parameters
> continuation    = yes           ; 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         = 10            ; 50 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)
> rlistlong       = 1.0           ; long-range neighborlist 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          = berendsen     ; Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 318   318     ; reference temperature, one for each
> group, in K
> nsttcouple      = 0.9999        ; 1 by default

Your value for nsttcouple makes no sense.  It needs to be an integer and should 
probably be left at the default of 1.

-Justin

> ; Pressure coupling is off
> pcoupl          = berendsen     ; Berendsen thermostat
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 1.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; assign velocities from Maxwell distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
> Could you please guide me to solve the problem?
>
>

-- 
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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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