Re: [ESPResSo-users] H_bond

[Stefan Kesselheim]

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