deisy yurley rodriguez sarmiento wrote:
Hi everyone,
I need help because when i run in gromacs, in a few seconds, appears
"segmentation fault" i think that posibly is die to .mdp file. So is
copied below. thanks in advance.
Well, a seg fault could be due to a large number of factors, although the .mdp
file is helpful. Generic information can be found here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
If you can provide more detail on what your system is, how you built it, what
Gromacs version you're using, and the success of energy minimization and
equilibration, that will help. Other comments are embedded within the .mdp file
itself.
title =
cpp = /usr/bin/cpp
include =
define = -DFLEXIBLE
Never use flexible water when running MD. It is only useful during energy
minimization, and doesn't make sense in the context of MD since all the default
water models are rigid. For instance:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
Maybe Gromacs should generate a warning about the combination of the md
integrator and the DFLEXIBLE parameter.
integrator = md
init = 0
dt = 0.001
nsteps = 500000
init_step = 0
comm-mode = Linear
nstcomm = 1
comm-grps =
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
nstxout = 100
nstvout = 100
nstfout = 0
nstcheckpoint = 1000
nstlog = 100
nstenergy = 100
nstxtcout = 0
xtc-precision = 1000
xtc-grps =
energygrps =
nstlist = 10
ns_type = simple
pbc = xyz
rlist = 1
domain-decomposition = no
coulombtype = shift
rcoulomb-switch = 0.9
rcoulomb = 1.0
epsilon_r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.0
DispCorr = No
table-extension = 1
energygrp_table =
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
Tcoupl = no
tc-grps =
tau-t =
ref-t =
Pcoupl = no
Pcoupltype = Isotropic
tau-p = 1
compressibility =
ref-p =
andersen_seed = 815131
QMMM = no
QMMM-grps =
QMmethod =
QMMMscheme = normal
QMbasis =
QMcharge =
QMmult =
SH =
tions =
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
MMChargeScaleFactor = 1
bOPT =
bTS =
annealing =
annealing_npoints =
annealing_time =
annealing_temp =
gen_vel = no
gen-temp = 300
gen-seed = 173529
constraints = none
constraint-algorithm = Lincs
unconstrained-start = no
Shake-SOR = no
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
energygrp_excl =
disre = simple
disre-weighting = Conservative
disre-mixed = no
disre_fc = 1200
disre-tau = 0
nstdisreout = 100
orire = no
orire-fc = 0
orire-tau = 0
orire-fitgrp =
nstorireout = 100
dihre = simple
dihre-fc = 100
dihre-tau = 0.0
nstdihreout = 50
free-energy = yes
init-lambda = 0
delta-lambda = 0
sc-alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3
You've got a combination of distance restraints, dihedral restraints, and free
energy calculations turned on. Is your system stable in the absence of all of
these factors?
-Justin
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000 ext. 2792
Universidad Industrial de Santander
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
