[gmx-users] NVT Equilibration error

[Tsjerk Wassenaar]

Hi Agnivo,

What is the rationale for ignoring the long bond warning?

Cheers,

Tsjerk
On May 5, 2015 17:41, "Agnivo Gosai" <agnivogromacs14 at gmail.com> wrote:

> Dear Users,
>
> I have a solvated protein-dna structure placed inside a simulation box.
> During topology preparation and subsequent steps I did not receive any
> warning , except a long bond warning in the pdb2gmx step for the protein.
>
> I then did an energy minimization. The script is shown below:
>
> ; For energy minimization
> ; Parameters describing what to do, when to stop and what to save
> integrator  = steep     ; Algorithm (steep = steepest descent minimization)
> emtol       = 500.0    ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps      = 500000     ; Maximum number of (minimization) steps to
> perform
> energygrps  = System    ; Which energy group(s) to write to disk
>
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist     = 1         ; Frequency to update the neighbor list and long
> range forces
> ns_type     = grid      ; Method to determine neighbor list (simple, grid)
> rlist       = 1.4       ; Cut-off for making neighbor list (short range
> forces)
> coulombtype = PME       ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.4       ; Short-range electrostatic cut-off
> rvdw        = 1.4       ; Short-range Van der Waals cut-off
> pbc         = xyz       ; Periodic Boundary Conditions
>
> This is the result at the end of the minimization :
>
> Steepest Descents converged to Fmax < 500 in 8938 steps
> Potential Energy  = -7.5707590e+06
> Maximum force     =  4.4626624e+02 on atom 2581
> Norm of force     =  3.2807171e+00
>
> Then I proceeded for a 5 ns NVT equilibration , with the following script :
>
> title       = NVT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 2500000    ; 5 ns
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 500       ; save coordinates every 1 ps
> nstvout     = 500       ; save velocities every 1 ps
> nstenergy   = 500       ; save energies every 1 ps
> nstlog      = 500       ; update log file every 1 ps
> nstxtcout   = 1000      ;
> ; 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       = 1.4      ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.4      ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.4       ; 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
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = DNA_Protein Water_and_ions    ; two coupling groups - more
> accurate
> tau_t       = 0.1     0.1                     ; time constant, in ps
> ref_t       = 300     300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> 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
> ; COM motion removal
> ; These options remove COM motion of the system
> nstcomm         = 10
> comm-mode       = Linear
> comm-grps       = System
>
> However the simulation crashed and the following error messages were
> received :
>
> step 103336: Water molecule starting at atom 369120 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 103336: Water molecule starting at atom 356715 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.6.7
> Source code file:
> /work/gb_lab/agosai/GROMACS/gromacs-4.6.7/src/mdlib/pme.c, line: 851
>
> Fatal error:
> 1 particles communicated to PME node 11 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
>
>
> Now, what can be going wrong in here ? Do I need to do more energy
> minimization , using other algorithms? Or , should I be heating up my
> system gradually to 300 K ( from 270 K , for e.g.) and then do a NVT
> equilibration at 300 K?
>
> Kindly suggest.
>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
> --
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