[gmx-users] Getting too much time to finish nvt equilibrium, why?

[Tsjerk Wassenaar]

Hi Surya,

We can't say from this information. The log files should give more insight.
Was the computer being used for something else at the same time?

Cheers,

Tsjerk
On Dec 7, 2015 05:52, "Seera Suryanarayana" <palusoori at gmail.com> wrote:

> Dear Gromacs Users,
>
> After energy minimization I have done nvt equilibrium for 1ns. It has taken
> 15 to 20 minutes when I done it previously. Same equilibrium I did day
> before yesterday and it has take almost one day. I have used the same work
> station in both equilibrium processes. I have used the following mdp file.
> System consists 129 residue length protein and more the three 3,00,000
> water molecules. Kindly check the mdp file and let me how to resolve this
> long lasting processes.
>
>
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 500000                ; 2 * 500000 = 1000 ps
> dt                  = 0.002             ; 2 fs
> ; Output control
> nstxout         = 5000          ; save coordinates every 10.0 ps
> nstvout         = 5000          ; save velocities every 10.0 ps
> nstenergy       = 5000          ; save energies every 10.0 ps
> nstlog          = 5000          ; update log file every 10.0 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
> cutoff-scheme   = Verlet
> ns_type             = grid              ; search neighboring grid cells
> nstlist             = 10                ; 20 fs, largely irrelevant with
> Verlet
> 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         = Protein Non-Protein   ; 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 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
>
>
> Thanks in advance
>
> Surya
> Graduate student
> India.
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