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Re: [ESPResSo] How to fill simulation box with copies of complex molecul
Re: [ESPResSo] How to fill simulation box with copies of complex molecule which was read in from file ?
Sun, 11 Apr 2010 13:11:49 +0200
KMail/1.12.2 (Linux/2.6.33; KDE/4.3.2; x86_64; ; )
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.
Martha-Schmidtmann-Str. 7 Phone: +49-160-9166-7532
D-70374 Stuttgart E-Mail: address@hidden