[gmx-users] Re: Molecule Jumps

darrellk at ece.ubc.ca darrellk at ece.ubc.ca
Tue May 19 01:16:35 CEST 2009

Hi All,
I just wanted to let you know how I resolved my problem, in case anyone
else experiences a similar problem in the future.

My structure spanned all four quadrants around the origin (i.e. the 4
vertices of my structure were (-x, -y), (-x,y), (x,-y), & (x,y)). I
think because it spanned all 4 quandrants, this caused the molecule to
jump from corner to corner within the box.

Once I translated my molecule such that its coordinates were entirely
within the positive x,y quandrant, the molecule no longer jumped around
in the box.

Best regards,

Darrell Koskinen

>Date: Sun, 17 May 2009 20:08:06 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] Molecule Jumps
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4A0FE206.4000502 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>darrellk at ece.ubc.ca wrote:
>> Hi All,
>> I have an array of molecules above a grapehene sheet in my simulation.
>> However, when I look at my trajectory file (.trr) in VMD the array of
>> molecules is split into 4 sections with each section located at what
>> looks to be the corners of the simulation box. And the graphene sheet
>> does not stay stationary as it should, but rather jumps from corner to
>> corner. I tried to resolve this problem by running the following command:
>> trjconv -f traj.trr -o trajout.trr -center -pbc nojump
>> However, this did not resolve the problem. Is there something else I need
>> to do to resolve this problem?
>No, some combination of options to trjconv should work. Sometimes two
>two separate invocations with separate options are needed.
>BTW "...does not stay stationary as it should" is not true... you're
>wanting a certain feature for your visualization convenience, and during
>the simulation GROMACS hadn't permitted you to choose which of the
>infinite equivalent possibilities it should present in the trajectory.
>You're choosing that now, *after* the fact.

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