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Re: [ESPResSo-users] help

From: mehdi ezatabadi
Subject: Re: [ESPResSo-users] help
Date: Mon, 18 Jun 2012 21:23:36 +0430

Dear Dr.Arnold

In the past step of my project I used the espresso command to make the neighbor list of particles to see if they made special structures. The command was:

set nbhood [analyze nbhood idParticle cutOffRadious]

In condensed material simulations I figured it out that lots of complementary bases would interact which a single base that is different from the physics of base pair(A_T     C_G) interactions. Now I dont know how to include it in Integration by Espresso. Usually in the tcl program we define the interactions among the types of particles. But now I should look at the particles at every step and then decide which particles interact with each other.


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