1. General topics
  3. Tutorial
  5. Segmentation fault g_fg2cg

unanswered Segmentation fault g_fg2cg

  • Landry
  • Landry's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
11 years 4 months ago #1310 by Landry
Segmentation fault g_fg2cg was created by Landry
Hello,

I would like to transform a CG system in all atom. So I start with "the reverse transformation tutorial".
I have installed the modified gromacs code and try to do the example. but I have a segmentation fault error during the f_fg2cg step :

g_fg2cg -pfg fg.top -pcg dppc_cg.top -c cg.gro -o fg.gro -n 0
calling cpp...
processing topology...
Generated 483 of the 1653 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.125
Generated 663 of the 1653 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 3 bonded neighbours for DPPC 109
Excluding 0 bonded neighbours for FG_W 981
#      BONDS:   5341
#   G96BONDS:   214
#   HARMONIC:   3924
#     ANGLES:   6213
#  G96ANGLES:   327
#      PDIHS:   1936
#     RBDIHS:   2616
#      IDIHS:   474
#       LJ14:   3447
#     DIHRES:   237
#     CONSTR:   11772
calling cpp...
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for DPPC 109
Excluding 1 bonded neighbours for W 981

Number of fg atoms 17429 
Number of cg atoms 2333 
Reading frames from gro file 'Generated by trjconv : Martini system from WALP.pdb t= 12000.00000', 2333 atoms.
Reading frame       0 time 12000.000   1356007475 
Name of CG water in topology should be W

Fg pre-structure computed !
Segmentation fault (core dumped)

Please Log in or Create an account to join the conversation.

  1. General topics
  3. Tutorial
  5. Segmentation fault g_fg2cg
Time to create page: 0.087 seconds