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[ESPResSo] changing the file "integrate.c"

From: n_nikoofard
Subject: [ESPResSo] changing the file "integrate.c"
Date: Wed, 11 Mar 2009 21:33:01 -0000 (UTC)
User-agent: SquirrelMail/1.4.9a

Dear all,

I'm trying to change Espresso files according the needs of my problem.

I'm working on polymer translocation, in which a polymer passes through a
nanopore on a membrane. I want to measure the time which takes for the
polymer to cross the pore. To find this, I put the first monomer at the
entrance of the pore and after some initialization, I force the polymer to
worm through the pore (by exerting an external electric field to monomers
in the pore). Finally when the last monomer passed the pore I stop the
simulation and save the time.

As it is seen I should monitor the position of the last monomer of my
polymer and stop the integration when it has passed the pore. If I want to
do this in my code I should use "integrate 1" to be able to check the
position of this monomer after each integration step which is
computationally very costly. I have tried to do this with simple changes
in the functions integrate_vv() and propagate_vel_pos() of the file
"integrate.c", but it seems not to work as I expect. It stops the
simulation when the "first" monomer reaches the other side of the pore!
Maybe it means that I don't know the correct way of telling Espresso about
the identity of particles.

I have attached my version of file "integrate.c". Changes can be found in
the lines: 358, 369, 451, 559, 560, 946, 947, 949, 950, 980, 981, 998, 999
and 1012. It would be nice if someone can give me an idea about this file
or any other way to solve this problem.

Many thanks,
Narges Nikoofard

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