Running several simulations, we have found a problem with the 'g_traj' utility. It doesn't finish properly the files it generates, and gives a segmentation fault. This is what we have done:
We are working with double precision. With the file .mdp that is at the end of the mail, we have used 'grompp_d' to generate the .tpr file:
grompp_d -maxwarn 1000 -f temp_prueba_mail-list_001_mdpmdp -c ../data/in/pep_ini.gro -r ../data/in/pep_ini.gro -p ../data/in/pep.top -o temp_prueba_mail-list_001_tpr.tpr
After that, we ran the simulation with 'mdrun_d':
mdrun_d -s temp_prueba_mail-list_001_tpr.tpr -o temp_prueba_mail-list_001_trr.trr -c ../data/out/gro_unconstr_1.00_000001.gro -g ../data/out/log_unconstr_1.00_000001.log -e temp_prueba_mail-list_001_edr.edr
Then we tried to get the coordinates of the atoms with 'g_traj_d':
g_traj_d -f temp_prueba_mail-list_001_trr.trr -s temp_prueba_mail-list_001_tpr.tpr -ox temp_prueba_mail-list_001_ox.xvg
At the terminal, we tell the program to get the coordinates from the group 0 (system), although the error appears also for other groups.
Here is where the problem appears. When the program is about to finish, it makes segmentation fault and ends abruptly. The .xvg file has only some of the last lines missing, but those are the lines we are interested in. We have tried different ways: we have used different number of steps, we have get velocities and forces instead of coordinates... and always the same problem appears.
We would be very thankful if someone could tell us what is going wrong.
Best wishes,
Jorge Alberto Jover Galtier
Universidad de Zaragoza, Spain
-----------------------
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001000
nsteps = 100000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = none
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1
nstvout = 1
nstfout = 1
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 1000
nstenergy = 1
nstcalcenergy = 1
; Output frequency and precision for xtc file
nstxtcout = 50
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = -1
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = no
; nblist cut-off
rlist = 20
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Reaction-Field-zero
rcoulomb-switch = 0
rcoulomb = 4
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdw-type = Shift
; cut-off lengths
rvdw-switch = 0
rvdw = 4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = no
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = 556380
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Shake
; Do not constrain the start configuration
unconstrained-start = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-5
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
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