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

[Justin Lemkul]

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?

-Justin

-- 
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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

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