[gmx-users] Segmentation fault 2

Fri Mar 7 12:25:17 CET 2003

Dear Christoph,

Before md, I’ve performed an energy minimization in my system until 1000
Kj/mol.nm and, than, a pr dynamics of 10 ps with all bonds constrained.
This two steps were successful.  
Following your suggestion I’m going to try to perform the dynamics with
no constraints.
            Thank you very much.
            Tanos C. C. Franca
            IME – Rio de Janeiro - RJ

Looks like you have some kind of strain in your system that causes the
lincs to crash.

How did you setup you system?
Have you performed a steepest decent run before the md?
Has the system alreday been equilibrated after solvatation/minimization?
If not try reducing the timestep and maybe turn of the constraints for
the first 10 or 20 ps.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

-----Mensagem original-----
De: Tanos C. C. França [mailto:tccf at epq.ime.eb.br] 
Enviada em: quinta-feira, 6 de março de 2003 11:18
Para: 'gmx-users at gromacs.org'
Assunto: Segmentation fault

            Dear users,       
            I´m trying to perform 50 ps of dynamics in an enzyme docked
to its coenzyme and cofactor but the calculation is halting in step 17
with the following message: “segmentation fault”. 
Does someone know what does it means ? I’m sending below my md.job and
md.mdp files.
            Thanks in advance for any help.

                                             MD.JOB FILE

Back Off! I just backed up mdlog.log to ./#mdlog.log.1#
Reading file trp_md.tpr, VERSION 3.1.4 (double precision)
Reading file trp_md.tpr, VERSION 3.1.4 (double precision)

Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun '? in water'
25000 steps,     50.0 ps.

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 10.850835 (between atoms 2168 and 2169) rms 0.243141
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2168   2169   90.0    0.1000   1.1851      0.1000
   9003   9004   90.0    0.1000   0.1783      0.1000
Warning: 1-4 interaction at distance larger than 4
These are ignored for the rest of the simulation
turn on -debug for more information

Step 17, time 0.034 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 9238773122.213078 (between atoms 2168 and 2169) rms 227068560.621634
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2164   2165   90.0    0.1000 422710940.3923      0.1000
   2168   2169   90.0    1.1851 923877312.3213      0.1000
   2436   2437   90.0    0.1000   1.3047      0.1000
   2436   2438   90.0    0.1000   0.2488      0.1000
   2436   2439   90.0    0.1000   0.6916      0.1000
   9003   9004   90.0    0.1783   0.3997      0.1000
   9095   9096   31.6    0.1000   0.1000      0.1000
[3]+  Segmentation fault      mdrun_d -s trp_md.tpr -o trp_md.trr -c
trp_b4md.gro -g mdlog 1>&md.job

                                                            MD.MDP FILE
;
;     User spoel (236)
;     Wed Nov  3 17:12:44 1993
;     Input file
title               =  PEP MD
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  hbonds
integrator          =  md
dt                  =  0.002   ; ps !
nsteps              =  25000   ; total 50ps
nstcomm             =  1
nstxout             =  500
nstvout             =  0
nstfout             =  0
nstlist             =  5
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
; Berendsen temperature coupling is on in three groups
Tcoupl              =  Berendsen
tau_t               = 0.1       0.1    0.1
tc-grps             = protein   drg    sol
ref_t               = 300       300    300
; Pressure coupling is not on
Pcoupl              = no
pcoupltype          = isotropic
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocities is on at 300 K
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529

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