Re: [ESPResSo] How to fill simulation box with copies of complex molecule which was read in from file ?

[Salvador Herrera Velarde]

Hi Marek,

I think there is another option although is not exactly what you want.

You can use mbtools package to introduce new molecules.  You should modify  place.tcl and maybe random.tcl. 

Both scripts are in 
mbtools/system_generation

cheers,

SHV


----- Original Message -----
From: Marek Maly <address@hidden>
Date: Monday, April 12, 2010 8:16 am
Subject: Re: [ESPResSo] How to fill simulation box with copies of complex molecule which was read in from file ?
To: address@hidden, address@hidden

> Dear Axel,
> 
> thank you very much.
> 
> I will do some "copy" function when I have little time (in few days)
> and send it to all.
> 
> Best,
> 
>      Marek
> 
> 
> 
> 
> 
> Dne Sun, 11 Apr 2010 13:11:49 +0200 Axel Arnold 
> <address@hidden> napsal/-a:
> 
> >On Sunday 11 April 2010, Marek Maly wrote:
> >>Dear all,
> >>
> >>let say that I prepare external block file with the structure 
> (positions,>>covalent bonds, types of particles) of
> >>one complex molecule X (let say specific hyperbranched polymer).
> >>
> >>If I use the right block format I should have no problems to 
> load this one
> >>molecule into espresso using
> >>blockfile command.
> >>
> >>But let say that I want to put into simulation box several of such
> >>molecules not just one.
> >>
> >>What is the best way how to do it in actual version of the 
> Espreso ?
> >>
> >>Is there for example some COPY command which is able to copy whole
> >>molecule X
> >>INCLUDING BONDS and put it in some shifted position in simul. 
> box ?
> >>
> >>If one does not care about the bonds, it is very trivial task.
> >>Also copying of the bonds should not be not so big problem
> >>just using "part $i print connections" to learn connectivity
> >>of the particles of original molecule and create the same 
> connections in
> >>particles which belong to new molecule. But OK, this approach 
> is possible
> >>but if there already exist some simple COPY function which is 
> capable to
> >>create
> >>copy of the original molecule (including all relevant 
> properties for
> >>example all, potentials (bond, angle, dihedral) )
> >>I would really prefer it.
> >
> >Hi!
> >
> >Not that I am aware of. At least when I was writing  our 
> benchmark scripts, I
> >did the copying manually... You can of course write a 
> corresponding Tcl
> >function and post it back, then we can include it in the 
> distribution if
> >someone needs such a copy function in the future.
> >
> >Cheers,
> >Axel
> >
> 
> 
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