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Re: [ESPResSo-users] H_bond

From: Stefan Kesselheim
Subject: Re: [ESPResSo-users] H_bond
Date: Thu, 28 Jun 2012 14:36:26 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20120421 Thunderbird/12.0

Dear Mehdi,

On 06/28/2012 01:43 PM, mehdi ezatabadi wrote:
Dear Friends

Would you know how to simulate H bond in Espresso? Mr.Kosovan suggested me to use new dynamical bonding feature of Espresso 3.1. Can anyone help me in more details.
First: Simulating H-Bonds is something difficult and nonstandard.

Espresso is made for coarse-grained simulation and you need to have a particular model in mind if you want to use Espresso. As soon as you have created this model, you can start implementing it in an Espresso Simulation. But please keep in Mind that Espresso is only a helper and can not guide you through the modelling process. It is your job as a scientist with interest/talent/experience to express the complex real world in a simplified way. The opposite can lead to serious scientific misconceptions: If you are guided by what the program offers, you are biased how you would model it.

Thus: Please stick to the literature with these questions. We can help you with the implementation, but only after you tell us, what the mathematical details of your model are.

Cheers and good luck
Stefan Kesselheim

Thanks. Mohammad

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