[gmx-users] Error in simulated annealing

[Justin Lemkul]

On 8/21/17 2:42 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
> I wanted to do simulated annealing and I set up the .mdp file as follow...
>
> title           = OPLS 4qam MD simulation
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 50000000      ; 2 * 50000000 = 500000 ps (100 ns)
> dt                  = 0.002             ; 2 fs
> ; Output control
> nstxout                 = 50000         ; save coordinates every 100.0 ps
> nstvout                 = 50000         ; save velocities every 100.0 ps
> nstenergy               = 50000         ; save energies every 100.0 ps
> nstlog                  = 50000         ; update log file every 100.0 ps
> nstxout-compressed  = 50000      ; save compressed coordinates every 100.0
> ps
>                                  ; nstxout-compressed replaces nstxtcout
> compressed-x-grps   = System    ; replaces xtc-grps
> ; Bond parameters
> continuation            = yes           ; Restarting after NPT
> 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
> scheme
> 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 on
> pcoupl                  = Parrinello-Rahman         ; Pressure coupling on
> in NPT
> pcoupltype              = isotropic                 ; uniform scaling of
> box vectors
> tau_p                   = 2.0                       ; time constant, in ps
> ref_p                   = 1.0                       ; reference pressure,
> in bar
> compressibility     = 4.5e-5                ; isothermal compressibility of
> water, bar^-1
> refcoord_scaling    = com
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
>
>
>
>
>
>
>
> *;simulated annealingannealing            = single
> periodicannealing-npoints  = 4 3annealing-time    = 0 4000 8000 12000 16000
> 20000 24000annealing-temp   = 300 310 315 330 320 310 300*
> when I executed the mdrun with above .mdp file I got following error.
>
>
>
> *Fatal error:First time point for annealing > init_t.  *
> Kindly tell me what could be the reason for the error.

Probably because you're starting from a previous run (continuation = 
yes), grompp is taking the initial time frame as the one found in the 
checkpoint file, so you can't start your annealing from t = 0 in that case.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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