[gmx-users] Is there sth. wrong with my pull code?

[程迪]

Hi, gmx-users

I have a 128 dopc lipid bilayer as group 0 and a 270 atom sio2 sphere
as group 1. Sio2 is put on the top of lipid bilayer

I want them get close together. But the simulation always crash down
with a signal 11 fault when I pull the group 1.
There's nothing strange in md.log and output on screen except the pull
code. I do not know what happend. I think
this might be something related to the pull code.

I've run energy minimization. I am using gromacs 4.0.7 and ubuntu 9.10
desktop. Both single and double precision version
are tested.

Thanks, any comments is appreciable.

Here is part of  md.log

   pull                 = constraint
   pull_geometry        = distance
   pull_dim (3):
      pull_dim[0]=0
      pull_dim[1]=0
      pull_dim[2]=1
   pull_r1              = 1
   pull_r0              = 1.5
   pull_constr_tol      = 1e-06
   pull_nstxout         = 500
   pull_nstfout         = 500
   pull_ngrp            = 1
   pull_group 0:
     atom (6912):
        atom[0,...,6911] = {0,...,6911}
     weight: not available
     pbcatom              = 3455
     vec (3):
        vec[0]= 0.00000e+00
        vec[1]= 0.00000e+00
        vec[2]= 0.00000e+00
     init (3):
        init[0]= 0.00000e+00
        init[1]= 0.00000e+00
        init[2]= 0.00000e+00
     rate                 = 0
     k                    = 0
     kB                   = 0
   pull_group 1:
     atom (270):
        atom[0,...,269] = {21279,...,21548}
     weight: not available
     pbcatom              = 21413
     vec (3):
        vec[0]= 0.00000e+00
        vec[1]= 0.00000e+00
   wall_ewald_zfac      = 3
   pull                 = constraint
   pull_geometry        = distance
   pull_dim (3):
      pull_dim[0]=0
      pull_dim[1]=0
      pull_dim[2]=1
   pull_r1              = 1
   pull_r0              = 1.5
   pull_constr_tol      = 1e-06
   pull_nstxout         = 500
   pull_nstfout         = 500
   pull_ngrp            = 1
   pull_group 0:
     atom (6912):
        atom[0,...,6911] = {0,...,6911}
     weight: not available
     pbcatom              = 3455
     vec (3):
        vec[0]= 0.00000e+00
        vec[1]= 0.00000e+00
        vec[2]= 0.00000e+00
     init (3):
        init[0]= 0.00000e+00
        init[1]= 0.00000e+00
        init[2]= 0.00000e+00
     rate                 = 0
     k                    = 0
     kB                   = 0
   pull_group 1:
     atom (270):
        atom[0,...,269] = {21279,...,21548}
     weight: not available
     pbcatom              = 21413
     vec (3):
        vec[0]= 0.00000e+00
        vec[1]= 0.00000e+00
        vec[2]= 0.00000e+00
     init (3):
        init[0]= 4.70133e+00; the distance showed on screen is just
this value. However, I set pull_dim = NNY, why there is a init[0]
component?
        init[1]= 0.00000e+00
        init[2]= 1.59859e+04; is it right?
     rate                 = 0.01; can rate be negative? I mean I want
distance decreased.
     k                    = 0
     kB                   = 0


Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chengdi at mail.ustc.edu.cn
Tel.: +86-15321055911