[gmx-users] (no subject)

Seera Suryanarayana palusoori at gmail.com
Mon Dec 7 06:30:11 CET 2015


Dear Gromacs Users,

Sorry for the same mail again. I haven't provide sufficient information in
previous mail.

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.

I have used the following command:
mdrun -deffnm nvt -nt 4          means one MPI thread and 4 openMPP
threads.

topol.top info:
[ molecules ]
; Compound        #mols
Protein_chain_A     1
SOL         300217
NA               11


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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