February 23, 2018

Anita Condic
Publishing Process Manager
InTechOpen Book: Molecular Dynamics

Dear Manager Condic,

Please find enclosed the revised version of the chapter (now) titled: “THE PERFORMANCE OF
THE ADMP MOLECULAR DYNAMICS AND SIMULATED ANNEALING ALGORITHM FOR
HYDROGEN—BONDED SYSTEMS” according to the kind Editor’s comments

1. The chapter focuses on the applications of Simulated Annealing (SA) and MD, particularly,
the Atom-Centered Density Matrix Propagation (ADMP) molecular dynamics model as strategies to
generate initial configurations to subsequent optimization calculations. A very good detailed review
of the modeling in this area is presented. The topic of the chapter is undoubtedly useful for
researchers using molecular dynamics.
R// We appreciate this positive comment

2. The content of the chapter, written at a high scientific level, however, can be improved.

- Although the title of the chapter corresponds to its content, however it is complex and long. It is
desirable to change it.
R// The title was changed:
“THE PERFORMANCE OF THE ADMP MOLECULAR DYNAMICS AND SIMULATED
ANNEALING ALGORITHM FOR HYDROGEN—BONDED SYSTEMS”
Former version:
"THE PERFORMANCE OF THE ATOM CENTERED DENSITY MATRIX PROPAGATION
MODEL AND SIMULATED ANNEALING ALGORITHM IN THE POTENTIAL ENERGY
SURFACE EXPLORATION OF HYDROGEN BOND STABILIZED HETEROCLUSTERS,"
- It is not possible to read formulas. Formulas are inserted in the text as pictures with low quality, so
the symbols in the formulas are not clear.

R// Please open the document employing Word (*.docx), where the equations can be modified with
the Equation tool. In fact, this option was employed to insert all equations. Besides, we also upload
the .pdf version of the document.
- A reference to the literature is desirable for the last sentence of the conclusion. (“Even, the SA
applicability in systems as big as viruses is already reported.”)
R// The reference 36 was cited at the required part.
“Even, the SA applicability in systems of considerable size as those found in viruses is already
reported [36].”

3. iThenticate report 0%
R// Good to know! �

4. The chapter is written according to InTech Author Guidelines, except for formulas.
R// Please see the answer to the comment 2

In addition, we revised the whole chapter again, rewritten some phrases and corrected some little
mistakes.

Thanks for all your comments, patient, and this big effort to publish this book and give us the
opportunity to contribute.

Authors