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Re: [ESPResSo-users] H_bond

From: mehdi ezatabadi
Subject: Re: [ESPResSo-users] H_bond
Date: Thu, 28 Jun 2012 17:52:26 +0430

Of course you are right. My reference in modeling is noticed below:

I simulate this model by Espresso, The results were near to the paper results, but there was a little problem. Grouping the neighborhood base pairs in condensed material simulations. Due to simulate interaction among base pairs A_T C_G I used lj none bonded feature. It was based on the referenced paper. But it is not suitable. My substituted model :
Using fene bond with the nearest neighbor base pair. And delete it when another base pair particle goes to nearer than the past particle and make a new bond and ......... I forced to use fene bond because this feature is not designed for none bonded potentials .....
It made my code so slow because I implemented it by tcl coding .... I try to find a suitable feature perhaps designed in the past.

Any way thanks for your attention, Mohammad      

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