[gmx-users] Translating my system using editconf causes my run to crash!
jalemkul at vt.edu
Thu Feb 7 02:54:01 CET 2013
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>
>> 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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users