Re: [ESPResSo] Interactions beads same molecule

[Jacob Kirkensgaard]

Hi Salvador

I'm not sure I've thought this completely through, but using the  
normal mbtools cross/tail interactions is probably not possible which  
is probably why you're asking I suppose :-).

Anyway, I guess you could use a 'fake' bonded potential which only  
acts 'intra'. Whether you are using tabulated or calculated potentials  
you could define a new one as the difference between your 'intra- 
chain' and your 'inter-chain' potentials. What you need to do then is  
make a modification to the place.tcl file (in system_generation.tcl in  
the mbtools directory somewhere) to make sure this new bonded  
potentail is set up between the right beads (if this is a lipid system  
for example, you might wanna specify that the potential acts only  
between tail beads or whatever it is you wanna do). If you look at the  
way the FENE and stiffness bonded interactions are set in the lipid  
procedure in the place.tcl file it should be fairly straightforward to  
do this.

Hope I'm making sense...else write again and I'll confuse you even more!

Best,
Jacob Kirkensgaard



On Apr 13, 2009, at 11:03 PM, Salvador Herrera Velarde wrote:

> Dear All,
>
> I would like to know if somebody have an idea how to set the forces  
> in ESPResSO (mbtools) between the same kind of beads in different  
> molecules (lipids) alike to those belonging to the same molecule.
>
> I am no thinking in a  mixture of lipids. I have  the same kind of  
> lipid, but I need to specify different interactions between  
> intrachain beads and interchain beads.
>
> Some ideas?
>
> Thanks a lot in advance,
>
> Salvador Herrera
>
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