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

[Justin A. Lemkul]

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: chengdi at mail.ustc.edu.cn
> 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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