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 <jalem...@vt.edu>
Subject: Re: [gmx-users] Translating my system using editconf causes
my run to crash!
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <51130939.2090...@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.abra...@gmail.com>
Subject: Re: [gmx-users] Translating my system using editconf causes
my run to crash!
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<CAMNuMAT6ofqGeJGGGNJ6KEhM++e5XKBf_w4kfPEfmcOJL=
v...@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.bagherzade...@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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
