[AMBER] Is there any guide/tutorial/review to decide input format for MD based on system under consideration

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Wed, 22 Aug 2012 11:16:34 +0530

Dear Amber community members.
I have a general very important question about the guidelines for setting
up a MD simulation with Amber (It is associated about understanding basic
concept for various systems).

This relates specifically to the input file format. I understand that we
should thoroughly look into the Amber, tutorials and AmberTools manual for

But my question is related to the science of MD not just how different
input sections can be used. Question is when to use them and why to use
them for a particular problem?

Let me rephrase the question:

My question is how to decide about the details of steps in an MD simulation
(min, heat, den, eq followed by production run) if say?,
1) I want to understand protein folding problem in a given peptide or
2) I want to follow motion of certain section of the a protein, which is
know to be very promiscuous and dynamic.
3) I want to do clustering after MD simulation to understand the PES for
the system better.

Will these and many other systems and questions associated with them demand
that different input files formats for above mentioned steps? I think they
should, but beyond this I'm clueless.

When I go through some of the important papers like
http://pubs.acs.org/doi/abs/10.1021/ct700119m and
http://dx.doi.org/10.1021/ct300284c *I find that detailed MD steps are
given in short, but reasons for doing so with respect to the systems under
consideration are not given (which we don't expect in a research article).*

But as a student of MD simulations who wants to learn what determines these
things, which *book, review or article*, I should look into. Will
information in Amber documents be sufficient?

Because the MD community in general has been doing great with all kinds of
protein, nucleic acids, lipids and even whole membranes. I suspect this
must have been answered somewhere, but I'm not able to find.

Please suggest and pardon me if the questions were silly.

Thank you.
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
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Received on Tue Aug 21 2012 - 23:00:03 PDT
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