[gmx-users] FW: protein split over boundary

[ana johari]

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?
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?
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> wrote:
>
>
>
>
> From: anahita [mailto:ana_j0000 at yahoo.com]
> Sent: Friday, April 01, 2011 1:13 PM
> To: '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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