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Re: [ESPResSo] How to fill simulation box with copies of complex molecul

From: Marek Maly
Subject: Re: [ESPResSo] How to fill simulation box with copies of complex molecule which was read in from file ?
Date: Mon, 12 Apr 2010 15:09:13 +0200
User-agent: Opera Mail/10.10 (Win32)

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.



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
copy of the original molecule (including all relevant properties for
example all, potentials (bond, angle, dihedral) )
I would really prefer it.


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.


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