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Re: [ESPResSo-users] Error that i am unable to understand

From: Dudo
Subject: Re: [ESPResSo-users] Error that i am unable to understand
Date: Fri, 15 Apr 2016 10:57:32 +0200

lol, i do that too.. :-)

On Thu, Apr 14, 2016 at 11:08 PM, Axel Arnold <address@hidden> wrote:

First of all, it is considered impolite to contact people directly just because you don’t receive an immediate reply on a mailing list.

Second, regarding your problem:

> I hope this email finds you well. I hope you guys can help me to solve the problem that I am stuck with. I am trying to simulate a polymer with 150 monomers in a sea of obstacles (crowded environment) which are of 'type 0'. I want the polymer to be such that the first 75 monomers are of type 1 then the next 75 are of type 0. These monomers should be connected by a FENE bond.
> In order to do so, I have tried to create a polymer with 75 monomers of type 1 particles and another polymer of 75 monomers of type 0 particles.
> i then connected them using the 'bond' command
> " part 74 bond 0 75"
> where 74 and 75 are the partid of last monomer of the first polymer and the first monomer of the second polymer respectively. (Can I do this?)

Well, technically yes, but physically, that is non-sense. What the polymer command does is to setup a self-avoiding, that is, random walk. So, if you put two random polymers into a simulation box, what is the expected distance between the end monomer of the first (74 in your case) and the starting one of the second? Something around 8, so much more than your maximal physically allowed bond length. And that is what Espresso tells you.

The solution is to create a single polymer of length 150 and just re-assign the type of the second half of particles. That is  probably what you want, because you get a sensible starting configuration.


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