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:  079020 葛艳艳
 

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        My harvest in reading this paper:

At present, I’m writing a program to study properties of molecules and atoms confined to pore or channels by computer simulations. I have to calculate the electrostatic interactions of my 1D systems, I write the code based on Chem. Phys. literature (Chem. Phys. Lett. 363 (2002) 604-609). But I still have some questions for the G(z)=0 term. Whether this term can be calculated together with the real-space summation or not ?Then how calculate the force for this term? Shall I just differentiate the potential term of the G(z)=0 or calculated the force together with the reciprocal-space summation? After I read this paper, it give me some answers and ideas .I rewrite the subroutines again and made some corrections. Now it seems that I can get the correct energy. In my calculations the system is composed of 1190 water molecules. The simulation tube length is 51 angstroms and the radius is 15 angstroms. The cutoff distance of the real space is 11.08 angstroms. The convergence parameter alpha is equal to 9.0/L and beta is equal to 0.3. The reciprocal-space cutoff radius, , is equal to 14.0. The calculated energy is about -12900 kcal/mol, i.e. about -10.84 kcal/mol per molecule. But the numerical error is still large, about 10 kcal/mol. And the G(z)=0 term is still the most time consuming, though I have tried several procedures from some numerical library. I think maybe I need to make some corrections in the subroutine of echarge.f, since the other subroutines are picked from the existed software which is proved to be right.

        A brief outline for this paper:

A)          Title: Ewald type summations of Coulomb interactions in computer simulations of a system with one-dimensional periodic boundary conditions

B)          Introduction:

I.              In molecular dynamics (MD) simulations one must take into consideration not only interactions of charges from the basic simulation box, but also interactions of the charges with their images from the simulation box replicas.

II.           Introduce the interaction energy function of the system with three-dimensional periodic boundary conditions

III.         Introduce the parameter of above energy function

IV.        In some cases one may encounter systems, which are finite in two directions. And then the author write how to deal with this situation and his experiment in brief.

C)          Coulomb interactions in a system with one-dimensional periodicity

In a system with one-dimensional periodicity the energy sums are also conditionally convergent and direct summation of the energy using this formula is slow. And then present the question.

I.              Briefly state the One-dimensional Ewald method (EW1D) and it’s function

II.           Present Modified one-dimensional Ewald method (EW1DM) and it’s function

III.         Present Three-dimensional Ewald method with correction term (EW3DC) and it’s function

D)          Efficiency of the summation methods

Take the three methods presented in Section 2 in MD simulations of acetone molecules confined to cylindrical silica pores in different situation.

I.              Present how to choose the parameter in EW1D and introduce it’s result

II.           Talk about the parameter in EW1DM and EW3DC and theirs result

III.         Discuss the advantages and disadvantages of the methods analyzing the energy expressions and comparing speed of numerical calculations in test molecular dynamics simulations.

E)           Conclusions

F)           reference

        Describe the organization and the development of every passage. Write in square bracket behind every paragraph [paragraph development by time]

Ewald type summations of Coulomb interactions in computer simulations

of a system with one-dimensional periodic boundary conditions

1. Introduction

1)          [paragraph development by cause]

2)          [paragraph development by cause]

3)          [by definition or explain?]

4)          [by example]

2. Coulomb interactions in a system with one-dimensional periodicity

[by example]

2.1. One-dimensional Ewald method (EW1D)

[by comparison and contrast]

2.2. Modified one-dimensional Ewald method (EW1DM)

[by comparison and contrast]

2.3. Three-dimensional Ewald method with correction term (EW3DC)

[by comparison and contrast]

3. Efficiency of the summation methods

1)          [by example]

2)          [by cause and effect]

3)          [by cause and effect]

4)          [by comparison and contrast]

4. Conclusions

[by comparison and contrast]

        writing characteristics

This paper has a clear structure;

More nouns (often abstract ones) than spoken English and fewer verbs have been used;

This paper almost always uses the general person (one), rarely uses first person (I, we) and never uses second person (you)and makes limited use of personal pronouns for cohesion (it, them), preferring other ways of achieving cohesion;

avoids colloquial vocabulary;

avoids words that have emotional or attitudinal connotations;

Position of adverbs is in the middle of sentences.

        All important sentence

Marked in purple

1.         Computational time scales approximately as (N is number of charges), and with increasing N the efficiency of the method becomes worse than that of theEW1DM method when computational time grows like .

2.         When this ratio is large, the method is inefficient, and for its value smaller than 0.05 efficiency of the method is similar to that of the EW1DM method.

3.         Advantages and disadvantages of the methods are discussed analyzing the energy expressions and comparing speed of numerical calculations in test molecular dynamics simulations.

4.         The EW1D method may be modified using two dimensional Fourier transform of the functions depending on off-axis distance in the term given by Eq. (8).

5.         In the expression one has triple sum over components of the reciprocal-space vector and square of structure factor, which contains single sum over charges. In other words one sum over charges and the series over k in Eq. (8) is replaced by two sums over the reciprocal-space vector components and.

6.         Corresponding maximum relative errors of the total interaction energy, arising from the electrostatic interactions, are smaller than 10-6 and 10-7, because total interaction energy of acetone molecules in the pores is about 235 kJ/mol [11].

7.         Using the EW1D method the convergence parameter and the reciprocal-space cut-off that give the accuracy kJ/mol are and,respectively, whereas forkJ/mol, the parameters are following: and The series over k in Eq. (8)

8.         Moreover, various optimization techniques [13,14], such as particle-mesh method, which are available for the conventional Ewald method may be applied, and an additional reduction in computational time may be obtained.

        All important words and corresponding Chinese

Marked in blue

1.         long-range electrostatic interactions(长程静电相互力)

2.         one-dimensional periodic boundary conditions（一维周期性边界条件）

3.         molecular dynamics simulations（分子动力学模拟）

4.         replicated （复制，镜像）

5.         infinite lattice（无限珊格）

6.         conditionally convergent（条件性收敛）

7.         real-space summation（实空间加和）

8.         minimum image（最小镜像距离）

9.         charged particles（带电粒子）

10.     dipole moment (偶极距)

11.     reciprocal-space cut-off radius（倒易空间截断半径）

12.     time-step（时间步长）

13.     reciprocal-space term（倒易空间项）

        All idioms

Marked in this color (idiomatic expression)(习惯的表达方式)

1.         Marked in this color (idiomatic expression)(习惯的表达方式)

2.        

3.         where describes position of the charge with respect to position of the charge; with,,integers is the lattice vector describing position of the simulation box replica, and the prime indicates that for the terms for must be omitted.

4.         In the above equations is the complementary error function [4], a is the convergence parameter whose value is chosen for computational convenience

Collocation (The second paragraph)

1.         To obtain the total interaction energy of the basic simulation box one must take into account the interactions of charges from the basic simulation box

2.         as in theEW3D method

3.         be calculated together with the real-space term,

4.         one has three parameters

5.         one may make similar modification of the other term for

6.        where V, similarly as in the EW1DM method, means volume of the simulation box with empty space

        Locate some articles and sentence tense  

Marked in this color(The third paragraph)

1.         The acetone molecule is represented by a rigid set of four Lennard-Jones (LJ) interaction sites

2.         the interaction parameters and site positions in the molecular frame used in the calculations are presented in Table I of Ref. [10].

3.         where is an arbitrarily small number. The left-hand sides of the inequalities (14) and (15) are dimensionless factors

4.        Efficiency of the methods may be characterized by the CPU times per simulation time-step（时间步长）

        What citation format does the author use?

A citation is that one author speaks or writes words taken from the conclusions or the points of a passage, a book or an author for reference. Then the author makes it as an example or to support his/her own argument.

A citation format can be classified into two types: Modern Language Association (MLA) and American Psychological Association (APA).

In this paper, the author uses MLA format.

        Gain after reading this paper

At first ,I want to say that  I learned a lot from our short English class, which including not only the knowledge of English but also the methods of using the corpus consultation (web site) etc. This class is practical.

By reading this paper seriously and paying more attention on the author’s professional expression ,I learned how to organize academic paper and the professional expression . One paper should have a clear structure; use more nouns (often abstract ones) than spoken English and fewer verbs; use right pronoun ; avoid colloquial vocabulary; avoid words that have emotional or attitudinal connotations. All what have been discussed above ,we can learn from this paper. In a word ,I learned a lot by reading this paper seriously.

It is necessary that we should read more papers before we can successfully write one. I think as long as we insist on this idea, sooner or later, we will have our owe outstanding paper.