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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 15 10:43:31 CEST 2012

On 15/06/2012 6:27 PM, Shima Arasteh wrote:
> 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?

The box could move, but it can't accelerate, else it wouldn't be an 
http://en.wikipedia.org/wiki/Inertial_frame_of_reference. I suspect the 
laws of motion necessary for the simulation to take place in the frame 
of the (accelerating) motion of the protein COM are more complex than 
those that take place in a simple inertial frame. So that is not done - 
which also avoids having to force the user to choose their inertial 
frame or GROMACS guessing what frame they want.

> Is it possible for box to be defined every step?, then the protein 
> would stay in the center of the box.

The box is defined at every step. If you want your solute to have a 
given relationship to the box every step you have to post-process your 
trajectory as my earlier link told you.


> 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
> -- 
> gmx-users mailing list gmx-users at gromacs.org 
> <mailto:gmx-users at 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-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120615/52da1ef9/attachment.html>

More information about the gromacs.org_gmx-users mailing list