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Re: [ESPResSo-users] Pronlems with FENE bond

From: Nairhita Samanta
Subject: Re: [ESPResSo-users] Pronlems with FENE bond
Date: Mon, 31 Aug 2015 17:40:05 +0530

Thank you Florian for your reply. Yes I would definitely answer in the mailing list from now on.

So is it like if I mention a bond-length for the polymer, the 'polymer' command will automatically put the monomers accordingly. In that case I don't need to "set the position" for the monomers. Or do I need to?

On Mon, Aug 31, 2015 at 4:33 PM, Florian Weik <address@hidden> wrote:
On Mon, Aug 31, 2015 at 12:54 PM, Nairhita Samanta <address@hidden> wrote:
I assumed this way all the particles will be in a distance approximately $b_l from each other. So how do I position the monomers? According to box length?

"set posx [expr $b_l*rand()]
set posy [expr $b_l*rand()]
set posz [expr $b_l*rand()]" is it defining all the monomers or just the starting one? I am confuse with this command.

On Mon, Aug 31, 2015 at 4:17 PM, Florian Weik <address@hidden> wrote:
you are putting all particles in a sphere of radius of $b_l about the origin. Is this really what you want?
If you have other interactions, for example a Lennard-Jones, this will probably explode, if you have a
typical time step.


The polymer command actually creates the particles, the positions are chosen by a random walk with step length $b_l (because you said so).
If you have no other interactions what you did should still work, maybe you need to reduce you time step.

Please answer to the mailing list and not to me personally ('Answer to all'), so everybody can read profit from the conversation.


Florian Weik, Dipl.-Phys.,
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-67703
Public Key 0x0562F11D Fingerprint 3294 6360 EC93 37A3 BD40  F597 0BAD 3AF8 0562 F11D

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