Re: [gmx-users] periodic boundary conditions pbc=xyz

2015-04-05 Thread Tushar Ranjan Moharana 
Hi Ming
Use *-pbc mol* while using trjconv. Anyway it is not another box.

Best Regards
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB, INDIA
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Re: [gmx-users] periodic boundary conditions pbc=xyz

2015-04-05 Thread Tsjerk Wassenaar 
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.t...@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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Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] periodic boundary conditions pbc=xyz

2015-04-05 Thread 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-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@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.t...@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
 --
 Gromacs Users mailing list

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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
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--
Tsjerk A. Wassenaar, Ph.D.
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