[gmx-users] FW: protein split over boundary

[Justin A. Lemkul]

ana johari wrote:
> Dear user,
> 
> Tanks for your attention ,I read about trjconv,but I want to know is it 
> necessary  to back to the exact fram befor molecule split happens and 
> then center the molecule by trjconv command?
> 

If the protein starts in the center of the box, just use trjconv in conjunction 
with your original .tpr file.  A suggested trjconv workflow is on the page 
Tsjerk pointed you to.

> The other point,if you attention to my value”edit conf  d=0.9 and during 
> MD rvdw=1..4” is it broke the rule of periodic boundary condition or not?
> 

In principle, no, as long as your box does not significantly deform.  Check with 
g_mindist -pi.

-Justin

> tanks
> 
> 
> 
> ------------------------------------------------------------------------
> *From:* Tsjerk Wassenaar <tsjerkw at gmail.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Fri, April 1, 2011 1:29:19 PM
> *Subject:* Re: [gmx-users] FW: protein split over boundary
> 
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> -TAW
> 
> On Fri, Apr 1, 2011 at 10:53 AM, anahita <ana_j0000 at yahoo.com 
> <mailto:ana_j0000 at yahoo.com>> wrote:
>  >
>  >
>  >
>  >
>  > From: anahita [mailto:ana_j0000 at yahoo.com <mailto:ana_j0000 at yahoo.com>]
>  > Sent: Friday, April 01, 2011 1:13 PM
>  > To: 'gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>'
>  > Subject: protein split over boundary
>  >
>  >
>  >
>  > Dear user,
>  >
>  > Hello, I appreciate if somebody help me. During the simulation of my 
> protein
>  > I didn’t get any error but after 1ns of MD
>  >
>  > my molecule was split over boundary in cubic box. it means some part 
> of it
>  > enter the other side of the box.
>  >
>  > At first,For decreasing the cost of simulation, in “editconf” command 
> I set
>  > the number “d” on 0.9  to decease the box size. I want to mention that
>  > during the calculation my rvdw is 1.4.
>  >
>  > I want to know instead of problem of visualization, the other things is
>  > fine?
>  >
>  > Best regards.
>  >
>  > A. johari
>  >
>  > --
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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
> --
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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