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

[Justin Lemkul]

On 2/7/13 2:56 PM, S. Alireza Bagherzadeh wrote:
> 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.
>

OK, then this is a very different question.  Your original post seemed to 
indicate that you were translating coordinates and doing so caused the 
simulation to crash.  In contrast, what is actually happening is that the 
simulation is crashing because it is moving in a manner you believe to be 
incorrect, and you are simply post-processing the result to try to see what's 
going on.  Is all of this correct?  We need to be clear and on the same page to 
be productive.

> 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.
>

Please post a full .mdp file.  Without it, there are too many things to guess at.

-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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