[gmx-users] protein near the edges of simulation box

[Tsjerk Wassenaar]

There is no box, so it can't move. There is a lattice specified by
three lattice vectors defining the periodicity. These vectors are
updated every step based on the pressure, if you use pressure
coupling. You can specify the protein to have no net center of mass
motion, by setting it as comm_grps in the .mdp file.

Cheers,

Tsjerk



On Fri, Jun 15, 2012 at 11:35 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Hi,
>
> All molecules diffuse. As such, proteins are expected to move about.
> Preventing them form doing so is essentially non physical, so you'd need a
> good and thought-through reason for doing so.
>
> Erik
>
> 15 jun 2012 kl. 10.27 skrev Shima Arasteh:
>
> Thanks.
> I read that it doesn't matter if the protein moves and even protrudes the
> box. It's OK, but there is a question here; why doesn't the box move rather
> than the protein?
> Is it possible for box to be defined every step?, then the protein would
> stay in the center of the box.
>
> Sincerely,
> Shima
> ________________________________
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, June 14, 2012 12:22 PM
> Subject: Re: [gmx-users] protein near the edges of simulation box
>
> On 14/06/2012 5:47 PM, Shima Arasteh wrote:
>
> Dear gmx friends,
>
> I put a protein in a simulation box filled of water molecules and entered
> the mdrun command. After the simulation, I found the protein near one of the
> edges of the box and not in center. What is the problem? Anyone may suggest
> me?
> Does it mean that the simulation is meaningless?
> I expect the protein to stay in the center of box and goes unfold by passing
> the time.
>
> See
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
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> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands