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)
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Message: 5
Date: Tue, 5 Feb 2013 22:21:05 +0100
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] Translating my system using editconf causes
my run to crash!
To: Discussion list for GROMACS users <[email protected]>
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[email protected]>
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On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh <
[email protected]> 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
--
========================================
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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