[gmx-users] Re: gmx-users Digest, Vol 28, Issue 63

[anwar at cdfd.org.in]

hi maria,
So, what parameters do I have to give in the mdp file for periodic boundary 
condictions, I thought just by applying the PBC through editconf will do 
the job. 
regards
Anwar
----------------------
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
anwar.m1 at gmail.com
-----------------------



---------REPLY TO-------------
Date:Mon Aug 21 18:00:08 GMT+08:00 2006
FROM: gmx-users-request at gromacs.org
To: gmx-users at gromacs.org
Subject: gmx-users Digest, Vol 28, Issue 63
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Today's Topics:

   1. Re: periodic boundary condition ( MGi? )


---------------------------------------------------------------------- 

Message: 1
Date: Mon, 21 Aug 2006 10:13:27 +0200
From: " MGi? " <magiofer at gmail.com>
Subject: Re: [gmx-users] periodic boundary condition
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
	<e6acc8ab0608210113v39c9b46doa36cd97dcb70b985 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

yes, they are sufficient. if I remember well, the flag -pbc does the
opposite job, it removes periodic boundary conditions. anyway, remember 
to include in your mdp file the parameters for the treatment of periodic 
bonudary conditions!

regards,

Maria


On 8/21/06, anwar at cdfd.org.in <anwar at cdfd.org.in> wrote:
>
> Dear users,
> I want to apply the periodic boundary condition. So, the following options 
> are sufficient or not?
>
> editconf_d -f xxx.gro -o xxx_box.gro -d 1.0 -c
>
> Or do we also have to give the option -pbc????
>
> regards
> Anwar
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
> -----------------------
>
>
>
> -
>
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