[gmx-users] periodic boundary conditions pbc=xyz

[Ming Tang]

Hi Tsjerk,

I defined only one box. I mean several atoms in one chain run out of the boundary, and I can see them in the box but not in the chain. So I think maybe they run to the nearby box because of the periodic boundary conditions.

Thanks,
Ming 

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar
Sent: Sunday, 5 April 2015 7:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] periodic boundary conditions pbc=xyz

Hi Ming,

You have another box in your (infinite) periodic system?

Cheers,

Tsjerk


On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear all,
>
> I did a simulation using periodic boundary conditions pbc=xyz. It 
> turns out that the box is defined too small, and some atoms go to another box.
> Does this affect the simulation result? If not, how to display the 
> real model (without separation) in VMD?
>
> Thanks in advance,
> Ming
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