[gmx-users] gromacs error

[Urszula Uciechowska]

Can anyone help me with this error file? I did not get the log file...


Back Off! I just backed up md.log to ./#md.log.5#
Reading file md10ns-2.tpr, VERSION 4.5.3 (single precision)

Reading checkpoint file md10ns.cpt generated: Mon Jul 21 20:45:14 2014


Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical,
 see the log file for details.


Will use 18 particle-particle and 14 PME only nodes
This is a guess, check the performance at the end of the log file
Making 2D domain decomposition 2 x 9 x 1

Back Off! I just backed up traj.trr to ./#traj.trr.5#

Back Off! I just backed up traj.xtc to ./#traj.xtc.5#

Back Off! I just backed up ener.edr to ./#ener.edr.5#

WARNING: This run will generate roughly 5776 Mb of data

starting mdrun 'Protein in water'
10000000 steps,  20000.0 ps (continuing from step 5000000,  10000.0 ps).

NOTE: Turning on dynamic load balancing


Writing final coordinates.

Back Off! I just backed up confout.gro to ./#confout.gro.1#

 Average load imbalance: 13.5 %
 Part of the total run time spent waiting due to load imbalance: 3.8 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X
0 % Y 98 %
 Average PME mesh/force load: 0.833
 Part of the total run time spent waiting due to PP/PME imbalance: 3.4 %


my input file:

 7.3.3 Run Control
integrator              = md                    ; md integrator
tinit                   = 0                     ; [ps] starting time for run
dt                      = 0.002                 ; [ps] time step for
integration
nsteps                  = 5000000               ; maximum number of steps
to integrate, 0.002 * 2,500,000 = 5,000 ps
comm_mode               = Linear                ; remove center of mass
translation
nstcomm                 = 1                     ; [steps] frequency of
mass motion removal
comm_grps               = Protein Non-Protein   ; group(s) for center of
mass motion removal
; 7.3.8 Output Control
nstxout                 = 2500000       ; [steps] freq to write
coordinates to trajectory
nstvout                 = 2500000       ; [steps] freq to write velocities
to trajectory
nstfout                 = 2500000       ; [steps] freq to write forces to
trajectory
nstlog                  = 100           ; [steps] freq to write energies
to log file
nstenergy               = 500           ; [steps] freq to write energies
to energy file
nstxtcout               = 500           ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision           = 1000          ; [real] precision to write xtc
trajectory
xtc_grps                = System        ; group(s) to write to xtc trajectory
energygrps              = System        ; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist                 = 1             ; [steps] freq to update neighbor
list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions in
all directions
rlist                   = 0.8           ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 0.8           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = cut-off       ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 0.8           ; [nm] distance for LJ cut-off
DispCorr                = EnerPres      ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing          = 0.12          ; [nm] grid spacing for FFT grid
when using PME
pme_order               = 4             ; interpolation order for PME, 4 =
cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl                  = v-rescale                     ; temperature
coupling with Nose-Hoover ensemble
tc_grps                 = Protein    Non-Protein        ; groups to couple
seperately to temperature bath
tau_t                   = 0.1        0.1                ; [ps] time
constant for coupling
ref_t                   = 310        310                ; [K] reference
temperature for coupling

; 7.3.15 Pressure Coupling
pcoupl                  = parrinello-rahman     ; pressure coupling where
box vectors are variable
pcoupltype              = isotropic             ; pressure coupling in
x-y-z directions
tau_p                   = 2.0                   ; [ps] time constant for
coupling
compressibility         = 4.5e-5                ; [bar^-1] compressibility
ref_p                   = 1.0                   ; [bar] reference pressure
for coupling

; 7.3.17 Velocity Generation
gen_vel                 = no            ; velocity generation turned off

; 7.3.18 Bonds
constraints             = all-bonds     ; convert all bonds to constraints
constraint_algorithm    = LINCS         ; LINear Constraint Solver
continuation            = yes           ; apply constraints to the start
configuration
lincs_order             = 4             ; highest order in the expansion
of the contraint coupling matrix
lincs_iter              = 1             ; number of iterations to correct
for rotational lengthening
lincs_warnangle         = 30            ; [degrees] maximum angle that a
bond can rotate before LINCS will complain
(END)

Best regards
Urszula Uciechowska



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