[gmx-users] FW: protein split over boundary

[ana johari]

dear user,
Tanks for your advice,
But the mdrun is know on the step of 33562880  but the protein was split at the 
first 1ns of MD. is it necessary to use “tpbconv” command and extract the *.tpr 
file just after first 1 ns and  then use trjconv –ur compact as command.
Best regards,




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Fri, April 1, 2011 2:52:53 PM
Subject: Re: [gmx-users] FW: protein split over boundary



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
>  >
>  > --
>  > gmx-users mailing list    gmx-users at gromacs.org 
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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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