[gmx-users] FW: protein split over boundary

[Tsjerk Wassenaar]

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