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Re: [ESPResSo-users] Need Help

From: Peter Kosovan
Subject: Re: [ESPResSo-users] Need Help
Date: Thu, 14 Jun 2012 10:40:35 +0200 (CEST)
User-agent: Alpine 2.00 (LNX 1167 2008-08-23)

Dear Mohammad

If you have in mind binding with the nearest neighbour particle of a given 
type, I think the new dynamical bonding feature of Espresso 3.1 should solve 
your problem on the technical side. But I am not really sure if it is the 
proper way of modeling hydrogen bonding. If you could be more specific about 
your model, we can help you more on how to set it up in Espreso.

Please send your questions to the mailing list and not to individual people. 
There are several reasons for it (see user guide for more details):

1. More people = more different views = better chance for a good answer.

2. No single person has enough time to answer all questions on the mailing 
list. The load should be distributed.

3. Other users might also be interested in a similar problem.



Peter KoŇ°ovan
Institute of Computational Physics
University of Stuttgart
Pfaffenwaldring 27
70569 Stuttgart

On Thu, 14 Jun 2012, mehdi ezatabadi wrote:

Dear Dr.Kesselheim

I have a problem with my project. I have a md simulation. I have two different 
bases that interact with each other with LJ
potential by the bellow command:

inter 3 4 lennard-jones $ljAtt_eps $ljAtt_sig $ljAtt_cut 0 0

To simulate H bond among these types of particles in every step I should have 
look for the nearest complementary base and
allow the particle to interact just by this nearest neighbor and exclude the 
other complementary neighbors in this step.
And iterate it in every step again. I dont know how to perform it in Espresso. 
I look at the tutorial but I could not find
any suitable command. I would be grateful if you guide me by this problem.

Thank you, Mohammad

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