About ions Representation in NAMD

From: yangbing00_at_mails.tsinghua.edu.cn
Date: Wed Sep 28 2005 - 06:40:45 CDT

Hi All,

I have a question about how to add ions to NAMD Smlaion systems as follows:

There are always many types of ions in Biological Systems, such as calcium ions,
sodium ions and phosphate groups. And there always exists interactions between
these ions and Proteins, such as in Bone the binding of Hydroxyapatite to Collagen
molecules is the fundamental functional structure and decides the basic property
of Bone.

So I want to know how to handle such ions in NAMD. Do I need to define all the
topology files and force-field parameters by myself? And how it can be relized?

Thank you!

Your sincerely

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