[gmx-users] removing PBC why?

[javier]

Hi again, and thank you very much K. Anton, but removing PBC, not an error,
why???

I thought that if I have had selected PBC, the simulation should be done
with PBC, does not it?


Thank you 

Javier

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Today's Topics:

   1. Re: PBC removing why? (Anton Feenstra)


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

Message: 1
Date: Tue, 16 Aug 2005 09:06:57 +0200
From: Anton Feenstra <feenstra at few.vu.nl>
Subject: Re: [gmx-users] PBC removing why?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <43019091.1060404 at few.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

JAVIER SACRISTAN wrote:

> Hi Gromacs people,
>  
> I'm working to perform molecular dynamics simulations of 27 polymer chains
in
> PBC and I have 
> found some problems.
>  
> After preliminary minimization and equilibration of one chain under PBC
and NPT
> by means of  trjconv I have extracted the coordinates for my polymer chain
( I
> am interested in some specific conformation=specific frame on the
trajectory
> file).
>  
> Then with genconf -f  trajout.gro -nbox 3 3 3 -dist 1 -rot -o peo27.gro  I
have
> built a cell with 27  chains.
> 
>  
> 
> Finally with 
> 
> grompp -f peo25.mdp -p peo25.top -c tpeo25.gro -o peo25.tpr I have
generated 
> tpr file.
> 
>  
> 
> But unfortunately when I run the simulation I have got this message on the
log
> file:
> 
>  
> 
> Removing PBC first time.

Not an error.

-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|


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