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Re: [ESPResSo] Interactions beads same molecule

From: Jacob Kirkensgaard
Subject: Re: [ESPResSo] Interactions beads same molecule
Date: Mon, 13 Apr 2009 23:32:32 +0200

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!

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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