[gmx-users] Wrote pdb files with previous and current coordinates step 0Segmentation fault

[Atila Petrosian]

Dear Gromacs users,

I am doing Tutorial being in the following address by Gromacs 5.0.5 (MD
simulation of Protein with CG force field):

http://md.chem.rug.nl/index.php/tutorials-general-introduction/proteins

In equilibration step, I encountered with the following error:

starting mdrun 'Martini system from 1UBQ.pdb'
25000 steps,    500.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 45.543803, max 243.084229 (between atoms 30 and 31)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     46     48   46.4    0.3300   1.9179      0.3300
     48     50   69.6    0.3100   0.6984      0.3100
     50     52   96.1    0.3100   2.0152      0.3100
     52     54   90.1    0.3100   0.3167      0.3100
     54     56   90.1    0.3100   2.8162      0.3100
     56     59   90.0    0.3100   2.1376      0.3100
     59     60   90.9    0.3100   0.2376      0.3100
     60     63   89.9    0.3100   1.0495      0.3100
     63     65   89.5    0.3100   0.6335      0.3100
     65     67   90.3    0.3100   1.5334      0.3100
     67     69   45.8    0.3100   0.4112      0.3100
      5      6   90.0    0.3100  35.4772      0.3100
      8      9  154.5    0.2700   2.3856      0.2700
      8     10   88.3    0.2700   2.5844      0.2700
      9     10   90.1    0.2700   2.2418      0.2700
     26     27   90.0    0.2600   4.4256      0.2600
     28     29   90.0    0.3100   3.1146      0.3100
     30     31   90.0    0.2600  63.4619      0.2600
     36     37   90.0    0.2650   0.7127      0.2650
     46     47   72.5    0.2600   8.8295      0.2600
     48     49   89.8    0.3100  12.4260      0.3100
     54     55   91.1    0.2650   0.8494      0.2650
     63     64   92.8    0.3100   0.9315      0.3100
     92     93   90.0    0.3100   0.8565      0.3100
     95     96   90.0    0.2700   3.8656      0.2700
     95     97   90.1    0.2700   1.8690      0.2700
     96     97   90.0    0.2700   3.9438      0.2700
    115    116   90.0    0.2600  23.4200      0.2600
    124    125   89.9    0.2700   1.8030      0.2700
    124    126   89.9    0.2700   2.3510      0.2700
    125    126   89.9    0.2700   1.4336      0.2700
    129    130   90.0    0.3100   0.4544      0.3100
    140    141   90.0    0.2600   7.5170      0.2600
    145    146   90.0    0.2700  13.1290      0.2700
    145    147   90.0    0.2700  12.8287      0.2700
    146    147   62.5    0.2700   4.2500      0.2700
    150    151   90.0    0.2650   1.6979      0.2650

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
-------------------------------------------------------------------------------

mdp file is as follows:

define           =  -DPOSRES
dt               =  0.02
nsteps           =  25000
nstxout          =  0
nstvout          =  0
nstlog           =  100
nstxout-compressed        =  100
compressed-x-precision    =  10
rlist            =  1.2
coulombtype      =  PME
rcoulomb         =  1.2
epsilon_r        =  15
vdwtype = Cut-off
vdw_modifier = Force-switch
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  v-rescale
tc-grps          =  Protein W
tau-t            =  1.0 1.0
ref-t            =  300 300
Pcoupl           =  parrinello-rahman
Pcoupltype       =  isotropic
tau-p            =  12.0
compressibility  =  3e-4
ref-p            =  1.0
refcoord_scaling =  all
cutoff-scheme    = Verlet
---------------------------------------------------------------

Any help will highly appreciated.