[gmx-users] Re: Re: Translating my system using editconf causes my run to crash!

[S. Alireza Bagherzadeh]

Dear Justin,

Today's Topics:
>
>    1. Re: Translating my system using editconf causes my run    to
>       crash! (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 06 Feb 2013 20:54:01 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Translating my system using editconf causes
>         my run  to crash!
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51130939.2090401 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 2/6/13 3:03 PM, S. Alireza Bagherzadeh wrote:
> > Dear Mark,
> >
> >
> >
> >
> >> Today's Topics:
> >>
> >>
> >>     4. Translating my system using editconf causes my run to     crash!
> >>        (S. Alireza Bagherzadeh)
> >>     5. Re: Translating my system using editconf causes my run to
> >>        crash! (Mark Abraham)
> >>
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >>
> >> Message: 5
> >> Date: Tue, 5 Feb 2013 22:21:05 +0100
> >> From: Mark Abraham <mark.j.abraham at gmail.com>
> >> Subject: Re: [gmx-users] Translating my system using editconf causes
> >>          my run to       crash!
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Message-ID:
> >>          <CAMNuMAT6ofqGeJGGGNJ6KEhM++e5XKBf_w4kfPEfmcOJL=
> >> vPvA at mail.gmail.com>
> >> Content-Type: text/plain; charset=ISO-8859-1
> >>
> >> On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh <
> >> s.a.bagherzadeh.h at gmail.com> wrote:
> >>
> >>> Hi everyone,
> >>>
> >>> I am using "editconf" to translate my system along the z-axis.
> >>>
> >>
> >> Why? mdrun doesn't care.
> >>
> >
> > Because I want to preserve the geometry of my system for the purpose of
> > visualization as well as some post-analysis code that I write.
> > I noticed that mdrun as an output gives an image of the simulation box
> that
> > sits on the origin and extends along the positive direction of the
> > coordinate axises.
> >
> > This might clarify what I mean:
> >
> > My initial configuration looks like this:
> >
> > GAS | WATER | ICE | WATER | GAS       (center of system at z-axis: z = 35
> > nm)
> >
> > My final configuration looks like this:
> >
> > TER | ICE | WATER | GAS GAS | WA        (center of system at z-axis: z =
> > dZ/2 = 14.32431)
> >
> > dZ is the simulation box length along the z-axis.
> >
>
> This all looks like a rather normal product of PBC.  It sounds like you're
> just
> repositioning the elements within the unit cell for visualization and
> post-processing; where does a new simulation come into play?
>

There is no new simulation!

My primary question is about why translation causes a simulation to crash!
This looks so strange and weird to me.

With regards to the above, I understand that this is the product of PBC but
I was not able to convert (TER | ICE | WATER | GAS GAS | WA) to my original
set up (GAS | WATER | ICE | WATER | GAS) using trjconv along with -pbc
option.


Regards,
Alireza




>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>