程迪 wrote:
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?
Certainly not, unless you have distances on the order of 15000 nm in your
system :)
rate = 0.01; can rate be negative? I mean I want
distance decreased.
A more robust approach is to use:
pull_geometry = direction
pull_vec1 = 0 0 -1
That way, you're pulling along the negative z-axis. Distances can't be
negative:
http://lists.gromacs.org/pipermail/gmx-users/2009-November/046720.html
You also have to make sure that the total distance you're pulling is less than
one-half of the z box vector to avoid PBC distances being measured spuriously.
-Justin
k = 0
kB = 0
Di Cheng
University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: [email protected]
Tel.: +86-15321055911
--
========================================
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
========================================
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