金属学报, 2020, 56(5): 795-800 DOI: 10.11900/0412.1961.2019.00305

金属Mg二阶锥面<c+a>刃位错运动特性的分子动力学模拟

李美霖1, 李赛毅,1,2

1.中南大学材料科学与工程学院 长沙 410083

2.中南大学有色金属材料科学与工程教育部重点实验室 长沙 410012

Motion Characteristics of <c+a> Edge Dislocation on the Second-Order Pyramidal Plane in Magnesium Simulated by Molecular Dynamics

LI Meilin1, LI Saiyi,1,2

1.School of Materials Science and Engineering, Central South University, Changsha 410083, China

2.Key Laboratory of Nonferrous Metal Materials Science and Engineering, Ministry of Education, Central South University, Changsha 410012, China

通讯作者: 李赛毅,saiyi@csu.edu.cn,主要从事金属塑性变形与织构的研究

收稿日期: 2019-09-16   修回日期: 2019-12-04   网络出版日期: 2020-04-23

基金资助: 国家自然科学基金项目.  51571213
湖南省自然科学基金项目.  2017JJ2312

Corresponding authors: LI Saiyi, professor, Tel: (0731) 88876621, E-mail:saiyi@csu.edu.cn

Received: 2019-09-16   Revised: 2019-12-04   Online: 2020-04-23

Fund supported: National Natural Science Foundation of China.  51571213
Natural Science Foundation of Hunan Province.  2017JJ2312

作者简介 About authors

李美霖,女,1991年生,硕士生

摘要

采用分子动力学方法模拟金属Mg的二阶锥面<c+a>刃位错在温度为300 K下的运动过程,研究不同大小及方向的外加剪切应力作用下的位错运动特性和结构演化规律。结果表明,实际驱动位错运动的有效剪切应力低于外加剪切应力;位错运动速率随外加剪切应力的增大而线性增大,在同等剪切应力下,对应于c轴拉伸变形时的位错运动速率高于c轴压缩,相应的拖曳系数显著高于同等温度下基面和柱面刃位错。位错运动特性的拉-压非对称性本质上与外加剪切应力对扩展位错宽度的影响有关。

关键词: 位错 ; 分子动力学 ; 滑移 ; 拖曳系数

Abstract

Magnesium has a hcp lattice structure, in which insufficient independent slip systems are available to accommodate applied plastic deformation at room temperature. The ductility of Mg is intimately related to the fundamental behaviors of pyramidal <c+a> dislocations, which are the major contributor to c-axis strain. In this study, the motion of <c+a> edge dislocation on the second-order pyramidal plane in Mg under external shear stress of different magnitudes and directions are simulated by molecular dynamics at 300 K, and the motion and structural evolution of dislocations are studied. The results show that the effective shear stress causing dislocation motion is lower than the external applied one and the dislocation velocity increases linearly with increasing applied shear stress. Under the same level of external shear stress, the dislocation velocity in shearing leading to c-axis tension deformation is higher than that for shearing leading to c-axis compression, and in both cases the corresponding viscous drag coefficients are significantly higher than those for basal and prismatic edge dislocations at the same temperature. The tension-compression asymmetry of dislocation motion is essentially related to the effect of applied shear stress on the extended dislocation width.

Keywords: dislocation ; molecular dynamics ; slip ; drag coefficient

PDF (1661KB) 元数据 多维度评价 相关文章 导出 EndNote| Ris| Bibtex  收藏本文

本文引用格式

李美霖, 李赛毅. 金属Mg二阶锥面<c+a>刃位错运动特性的分子动力学模拟. 金属学报[J], 2020, 56(5): 795-800 DOI:10.11900/0412.1961.2019.00305

LI Meilin, LI Saiyi. Motion Characteristics of <c+a> Edge Dislocation on the Second-Order Pyramidal Plane in Magnesium Simulated by Molecular Dynamics. Acta Metallurgica Sinica[J], 2020, 56(5): 795-800 DOI:10.11900/0412.1961.2019.00305

Mg及其合金具有比重轻、比强度高、刚度大和减震性良好等一系列优点,在汽车行业和航空航天等领域具有广阔的应用前景[1]。然而,与立方结构金属相比,Mg是典型的hcp结构,室温下可启动的滑移系少,塑性变形能力较差[2]。为了克服Mg塑性较差的缺点,近年来关于Mg变形机制的研究已成为重要的研究课题[3],而位错运动特性是进一步在微观尺度研究位错相互作用及其结构变化,在细观尺度定量描述滑移变形机制的重要基础[4]。分子动力学(molecular dynamics,MD)可通过模拟原子运动、记录原子运动轨迹以及利用统计力学方法计算得到多体系统的静态和动态特性[5],因而成为研究位错运动特性的有效计算方法[6]

目前,仅有Groh等[7]和Fan等[8,9]基于MD探讨了Mg常见滑移系上的位错运动特性。其中,Groh等[7]研究了在100~500 K下的基面和柱面<a>刃、螺位错,以及100 K下一阶锥面<a>刃位错的运动规律,计算了在黏滞拖曳机制控制下定量表征位错可动性的拖曳系数。Fan等[8]模拟了初始温度为0 K的二阶锥面(Py-II)<c+a>刃位错的运动,发现位错运动速率随外加剪切应力增大而增大,且不同剪切方向对应的位错运动速率存在差异。进一步研究[9]发现,温度对Py-II<c+a>刃位错的临界分切应力(CRSS)有明显影响。总体上,在这些Mg的常见滑移系中,关于Py-II<c+a>刃位错运动特性的研究相对较少,尤其缺乏对其在常见加工温度下位错运动速率与外加剪切应力相关性及位错可动性的研究。Py-II<c+a>位错滑移是协调c轴方向应变的重要机制[10],研究这一机制对改善Mg及其合金的力学性能具有重要意义。

本工作采用MD方法模拟在给定温度和一定外加剪切应力范围内Mg中Py-II<c+a>刃位错运动,研究外加剪切应力的大小及方向对位错运动速率和芯结构的影响,探讨相关位错滑移行为的物理本质,并计算黏滞拖曳机制下的位错可动性,以期补充Mg常见滑移系的位错运动特性结果,为变形机制的研究提供参考。

1 模拟方法

一般认为塑性变形的控制机理主要有3种:热激活位错运动、黏滞拖曳和相对论效应机制[11]。这些机理所对应的位错运动速率随外加剪切应力变化趋势显著不同。对于纯金属刃位错运动,热激活机制对应的位错运动速率随剪切应力增加而呈指数增加,但最大速率往往不超过10-3倍的剪切波波速(Cs)[12]。由热激活机制过渡到黏滞拖曳机制后,位错运动速率可以达到约0.8Cs,与外加剪切应力呈线性关系[13]。进入相对论效应机制所控制的阶段后,位错运动速率接近于Cs,随剪切应力的增加而无明显变化。黏滞拖曳机制对应的位错运动速率与常规金属塑性加工过程最为相关,是目前研究位错运动特性的主要内容。

本研究重点考察黏滞拖曳机制控制下的位错运动特性。为此,需要模拟单个位错在不同外加剪切应力下的运动。模拟采用开源软件Lammps[14],所建刃位错运动模型如图1所示。参考文献[15]的设置,将模型沿y方向分为顶部、中部和底部3个区域。其中,顶部区域内的原子不能沿y方向运动,但可在xz平面内运动;底部区域内原子固定不动;中部区域内的原子可以沿任意方向运动。y方向设定为固定边界条件,xz方向为周期性边界条件(periodic boundary condition,PBC)。对于Py-II<c+a>刃位错,x方向平行于刃位错的Burgers矢量方向[112¯ 3¯],y方向平行于滑移面(图中蓝色面)法线方向[112¯2],z方向平行于[11¯00]。模型尺寸为30.2 nm (x)×30.0 nm (y)×10.0 nm (z),顶部和底部区域沿y方向厚度均为1.5 nm,系统内的原子总数约为392000。

图1

图1   刃位错运动模型示意图

Fig.1   Schematic of the model for the motion of an edge dislocation

Color online


基于上述刃位错模型和Kim等[16]的修正型嵌入原子势,模拟了温度为300 K下的位错运动。首先,采用共轭梯度法进行能量最小化弛豫。然后,在等温等压(NPT)系综下进行温度和压力调控,使体系温度达到目标温度且稳定、PBC方向(即xz方向)上的应力趋近于零,升温速率约为1.0 K/ps,在后续保温过程中增大固定边界方向(即y方向)的模型尺寸(增大量约为0.27 nm)以充分消除升温后该方向的正应力。最后,在微正则(NVE)系综下,通过向顶部区域的原子施加外力的方式,分别施加沿x轴正、负方向的剪切应力(目标值为0~250 MPa,时间步长为0.002 ps),使位错沿不同方向滑移(正、负剪切分别导致c轴压缩和拉伸),同时采用Berendsen恒温器进行温度控制[17],实际温度波动范围不超过±5 K。为避免加载速率过高而使晶体产生强烈的惯性效应[18],外加剪切应力增速控制在1.0 MPa/ps以下,达到目标应力值后运行至少100 ps以获得剪切应力和温度都相对稳定的位错运动速率。

2 结果与讨论

2.1 有效剪切应力

在位错运动过程中,尽管大部分外力做功转变为系统内原子的动能和势能,但还有少部分以内能的形式耗散,因而实际驱动位错运动的剪切应力(即有效剪切应力(τeff))往往与外加剪切应力(τapp)存在一定差异[19]。在定量分析位错运动特性时,有必要考察τeff偏离τapp的程度。

图2a以正剪切为例,给出了不同τapp下模型内的τeff随模拟时间(t)的变化曲线。其中,τeff在数值上等于根据Virial定理计算的体系的剪切应力分量(τxy)[20]。可以看出,τeff进入相对稳定阶段后(如τapp=50 MPa时,t=60~160 ps),没有出现由于惯性效应所导致的大幅振荡,稳态阶段的τeff略低于τapp。由图2b所示稳态阶段平均有效剪切应力(τ¯eff)τapp的变化可以进一步看出,τ¯effτapp之间表现为正线性相关,采用最小二乘法进行线性拟合所得斜率约为0.92 (即τ¯eff≈0.92τapp)。在后续定量讨论位错运动特性时,将采用τ¯eff以排除模拟过程中外力做功伴随的内能耗散对结果的潜在干扰。

图2

图2   正剪切下有效剪切应力(τeff)和平均有效剪切应力(τ¯eff)随外加剪切应力(τapp)的变化

Fig.2   Variations of effective shear stress (τeff) (a) and average effective shear stress (τ¯eff) (b) with the applied shear stress (τapp) under positive shear (t—time)


2.2 位错运动特性

位错在单位时间内的位移量与τapp有关,根据位错运动过程中位错芯的位移(d)-t变化,可以考察其基本运动特性。图3以正剪切为例,给出了不同τapp下Py-II<c+a>刃位错芯的dt的变化曲线。其中d取位错芯结构内所有原子位移的平均值。可以看出,不同τapp条件下,d都是先随t的延长而缓慢增大,然后逐渐转变为线性增长,即相应的位错运动速率趋于稳定。图中箭头所指点是图2a所示τeff进入相对稳定阶段的起始时刻。对比图2a和3可以发现,位错运动速率的稳定阶段与τapp (或相应的τeff)的稳定阶段一致。

图3

图3   不同τapp (正剪切)下位错芯的位移(d)-时间(t)曲线

Fig.3   Displacement (d)-t curves for the dislocation core under different τapp (positive shear) (The arrows indicate the starting points when τeff enters into a relatively stable stage as shown in Fig.2a)


为了定量分析τ¯eff (或相应的τapp)对位错运动的影响,图4给出了分别施加正、负剪切应力时,Py-II<c+a>刃位错的运动速率(v)与τ¯eff的关系曲线。v通过线性拟合τeff相对稳定阶段的d-t数据来确定。可以看出,无论正剪切(c轴压缩)或负剪切(c轴拉伸),v都随τ¯eff的增加而线性增大,符合黏滞拖曳机制控制下的位错运动规律。事实上,本研究模拟所达到的最大v值约为0.88 nm/ps,远低于Mg的Cs (3.12 nm/ps)[7],属于黏滞拖曳机制控制的速率范围。其次,在同等τ¯eff水平下,负剪切所得v略高于正剪切,呈现出拉-压非对称性,且差异随τ¯eff的增加而扩大。Fan等[8]在较大外加剪切应力范围内研究了初始温度为0 K下该位错的运动特性,结果显示出较弱的拉-压非对称性,但他们计算的v并非随τapp的增加而线性增大,拉-压非对称性程度随τapp的变化亦更为复杂,且模拟过程伴随有较明显的温升。由此看来,Py-II<c+a>刃位错运动特性的拉-压非对称性不但与剪切应力水平有关,还可能随温度的变化而变化。

图4

图4   正、负剪切时位错运动速率(v)随τ¯eff的变化曲线

Fig.4   Dislocation velocity (v) as a function of τ¯eff under positive shear and negative shear


根据位错运动理论,黏滞拖曳机制控制位错运动时,v与施加在位错上的剪切应力呈线性关系[21]。排除外力做功时内能耗散的干扰,考虑实际驱动位错运动的剪切应力τ¯eff,则vτ¯eff之间满足以下方程:

Bv = (τ¯eff-τp')b

式中,b是位错Burgers矢量模;B是拖曳系数,定量表征黏滞拖曳机制控制下的位错可动性,即B越大则可动性越低;τp'是对vτ¯eff进行线性拟合时的横截距,体现黏滞拖曳机制下启动位错滑移需要克服的阻力。利用式(1),采用最小二乘法对图4v-τ¯eff数据进行拟合,获得正、负剪切条件下的τ¯eff/v分别为2.77和2.54 Pa·s/nm,对应的B分别为1.69×10-4和1.55×10-4 Pa·s,显著高于同等温度下基面、柱面<a>刃位错的B值(不大于3.50×10-5 Pa·s[7])。因此,Py-II<c+a>刃位错的可动性相对较低。同时,不同剪切方向下较为明显的B值差异则表明,该位错运动的拉-压非对称性可能是引起Mg及其合金宏观拉-压非对称性的重要因素。

2.3 位错芯结构的演化

位错运动特性与位错结构的演化密切相关。研究发现,在能量最小化弛豫后,Py-II<c+a>刃位错已经分解成2个以内禀型层错区相连的不全位错(Burgers矢量模均为1/2<c+a>的刃型位错),形成扩展位错。图5是分别施加正、负剪切时,不同τapp作用下Py-II<c+a>刃位错在稳态阶段的位错芯结构。这些截面图对应于沿模型z方向一个周期内(共4层)的原子。原子畸变程度及所属晶体结构类型的判别均采用Ovito软件完成[22,23]。可以看出,在外加载荷作用下,扩展位错的基本特征没有改变,但在位错运动过程中2个不全位错的结构始终存在不同程度的差异。基于此类截面图,结合刃位错多余半原子面特征,可以进一步确定2个不全位错的中心位置,其间距即为扩展位错宽度(l),该值可定量体现位错芯结构变化的重要特征[24]。这些结果初步显示,在位错运动过程中,lτapp的变化而发生明显变化,而且相同τapp下不同剪切方向所对应的l值亦存在差异。

图5

图5   不同τapp下的位错芯结构

Fig.5   Dislocation core structures under τapp=50 MPa (a1, b1), τapp=150 MPa (a2, b2) and τapp=250 MPa (a3, b3) (l—width of extended dislocation, b—modulus of Burgers vector)

(a1~a3) positive shear (b1~b3) negative shear


为了系统分析τapp的大小及方向对位错芯结构的影响规律,以进一步理解位错运动特性,图6给出了分别施加正、负剪切应力时不同τapp作用下Py-II<c+a>刃位错芯结构的l值变化情况。这些l值是τeff进入稳定阶段70 ps后,在30 ps内(如τapp=50 MPa时,t=130~160 ps)每1.0 ps提取一次所获l值的平均值,图中所示误差范围为对应时间段内的标准差。可以看出,尽管原子热运动导致l值显著波动,但该值随τapp大小及方向的变化呈现出一定的规律,即:在正剪切过程中随τapp的增大而减小,负剪切时则随τapp的增大而增大;相应地,正、负剪切所对应的l值差异随τapp的增大而变得更加显著。根据位错运动阻力的相关理论,扩展位错的晶格阻力与其宽度呈负相关[25]。上述结构演变特征可以在一定程度上解释位错的运动特性。例如,相同τapp下负剪切所得v高于正剪切的结果可以归结于前者导致较大的l,相应的晶格阻力较小;正、负剪切所得v的差异随τapp的增加而扩大的现象则是由于正、负剪切所得l的差值增加,相应的晶格阻力差异增大。

图6

图6   正、负剪切过程中扩展位错宽度(l)随τapp的变化

Fig.6   Variations of l with τapp under positive shear and negative shear


有少量研究[8,26]模拟了Py-II<c+a>刃位错在0 K时的运动及其结构演化。其中,Fan等[8]考察了τapp=0 MPa条件下的位错结构,得到的l值为2.14 nm。该值与本研究在300 K、0 MPa时的l值(2.17 nm,图6)非常接近。另外,Kumar等[26]发现,当剪切应变达到0.5%时,正、负剪切所对应的l值亦存在明显差异,分别为1.96和2.56 nm,这一结果与本研究τapp=150 MPa时的结果较为接近。由此看来,尽管Py-II<c+a>刃位错在不同温度下的结构演变呈现类似的特征,但拉-压非对称性的程度则与外加剪切应力(或应变)的水平有关。

3 结论

(1) Py-II<c+a>刃位错的运动速率随外加剪切应力的增大而线性增大,符合黏滞拖曳机制控制的位错运动特征。

(2) Py-II<c+a>刃位错表现出较为明显的拉-压非对称性,且其可动性显著低于基面或柱面刃位错:同等剪切应力水平下,正剪切(对应于c轴压缩)的位错运动速率低于负剪切(对应于c轴拉伸),相应的拖曳系数分别为1.69×10-4和1.55×10-4 Pa·s。

(3) Py-II<c+a>刃位错的扩展位错宽度在正剪切时随外加剪切应力增加而减小,在负剪切时则呈现相反的趋势。较高外加应力水平下正、负剪切所得位错运动速率差异增大,本质上与扩展位错宽度差异扩大有关。

参考文献

Pollock T M.

Weight loss with magnesium alloys

[J]. Science, 2010, 328: 986

DOI      URL     PMID      [本文引用: 1]

Chen Z H. Wrought Magnesium Alloy [M]. Beijing: Chemical Industry Press, 2005: 48

[本文引用: 1]

陈振华. 变形镁合金 [M]. 北京: 化学工业出版社, 2005: 48

[本文引用: 1]

Liu B Y, Liu F, Yang N, et al.

Large plasticity in magnesium mediated by pyramidal dislocations

[J]. Science, 2019, 365: 73

DOI      URL     PMID      [本文引用: 1]

Lightweight magnesium alloys are attractive as structural materials for improving energy efficiency in applications such as weight reduction of transportation vehicles. One major obstacle for widespread applications is the limited ductility of magnesium, which has been attributed to [Formula: see text] dislocations failing to accommodate plastic strain. We demonstrate, using in situ transmission electron microscope mechanical testing, that [Formula: see text] dislocations of various characters can accommodate considerable plasticity through gliding on pyramidal planes. We found that submicrometer-size magnesium samples exhibit high plasticity that is far greater than for their bulk counterparts. Small crystal size usually brings high stress, which in turn activates more [Formula: see text] dislocations in magnesium to accommodate plasticity, leading to both high strength and good plasticity.

Bertin N, Tomé C N, Beyerlein I J, et al.

On the strength of dislocation interactions and their effect on latent hardening in pure magnesium

[J]. Int. J. Plast., 2014, 62: 72

[本文引用: 1]

Jiang J J, Miao L, Liang P, et al. Computational Material Science—Design Practice Method [M]. Shanghai: Higher Education Press, 2010: 162

[本文引用: 1]

江建军, 缪 灵, 梁 培. 计算材料学——设计实践方法 [M]. 上海: 高等教育出版社, 2010: 162

[本文引用: 1]

Bacon D J, Osetsky Y N, Rodney D.

Chapter 88 dislocation-obstacle interactions at the atomic level

[J]. Dislocations Solids, 2009, 15: 1

[本文引用: 1]

Groh S, Marin E B, Horstemeyer M F, et al.

Dislocation motion in magnesium: A study by molecular statics and molecular dynamics

[J]. Modell. Simul. Mater. Sci. Eng., 2009, 17: 075009

[本文引用: 4]

Fan H D, El-Awady J A.

Towards resolving the anonymity of pyramidal slip in magnesium

[J]. Mater. Sci. Eng., 2015, A644: 318

[本文引用: 5]

Fan H D, Wang Q Y, Tian X B, et al.

Temperature effects on the mobility of pyramidal <c+a> dislocations in magnesium

[J]. Scr. Mater., 2017, 127: 68

[本文引用: 2]

Obara T, Yoshinga H, Morozumi S.

{112¯2}<1¯1¯23> slip system in magnesium

[J]. Acta Metall., 1973, 21: 845

[本文引用: 1]

Meyers M A, translated by Zhang Q M, Liu Y, Huang F L, et al. Dynamic Behavior of Materials [M]. Beijing: National Defense Industry Press, 2006: 230

[本文引用: 1]

(Meyers M A著>, 张庆明, 刘 彦, 黄风雷等. 材料的动力学行为 [M]. 北京: 国防工业出版社, 2006: 230

[本文引用: 1]

Mordehai D, Ashkenazy Y, Kelson I, et al.

Dynamic properties of screw dislocations in Cu: A molecular dynamics study

[J]. Phys. Rev., 2003, 67B: 024112

[本文引用: 1]

Olmsted D L, Hector L GCurtinJr, , et al.

Atomistic simulations of dislocation mobility in Al, Ni and Al/Mg alloys

[J]. Modell. Simul. Mater. Sci. Eng., 2005, 13: 371

[本文引用: 1]

Plimpton S.

Fast parallel algorithms for short-range molecular dynamics

[J]. J. Comput. Phys., 1995, 117: 1

[本文引用: 1]

Osetsky Y N, Bacon D J.

An atomic-level model for studying the dynamics of edge dislocations in metals

[J]. Modell. Simul. Mater. Sci. Eng., 2003, 11: 427

[本文引用: 1]

Kim K H, Jeon J B, Lee B J.

Modified embedded-atom method interatomic potentials for Mg-X (X=Y, Sn, Ca) binary systems

[J]. Calphad, 2015, 48: 27

[本文引用: 1]

Berendsen H J C, Postma J P M, van Gunsteren W F, et al.

Molecular dynamics with coupling to an external bath

[J]. J. Chem. Phys., 1984, 81: 3684

DOI      URL     [本文引用: 1]

Fan H D, El-Awady J A, Wang Q Y.

Towards further understanding of stacking fault tetrahedron absorption and defect-free channels—A molecular dynamics study

[J]. J. Nucl. Mater., 2015, 458: 176

DOI      URL     [本文引用: 1]

Cho J, Molinari J F, Anciaux G.

Mobility law of dislocations with several character angles and temperatures in FCC aluminum

[J]. Int. J. Plast., 2017, 90: 66

[本文引用: 1]

Thompson A P, Plimpton S J, Mattson W.

General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions

[J]. J. Chem. Phys., 2009, 131: 154107

DOI      URL     PMID      [本文引用: 1]

Three distinct forms are derived for the force virial contribution to the pressure and stress tensor of a collection of atoms interacting under periodic boundary conditions. All three forms are written in terms of forces acting on atoms, and so are valid for arbitrary many-body interatomic potentials. All three forms are mathematically equivalent. In the special case of atoms interacting with pair potentials, they reduce to previously published forms. (i) The atom-cell form is similar to the standard expression for the virial for a finite nonperiodic system, but with an explicit correction for interactions with periodic images. (ii) The atom form is particularly suited to implementation in modern molecular dynamics simulation codes using spatial decomposition parallel algorithms. (iii) The group form of the virial allows the contributions to the virial to be assigned to individual atoms.

Regazzoni G, Kocks U F, Follansbee P S.

Dislocation kinetics at high strain rates

[J]. Acta Metall., 1987, 35: 2865

[本文引用: 1]

Stukowski A.

Visualization and analysis of atomistic simulation data with ovito-the open visualization tool

[J]. Modelling Simul. Mater. Sci. Eng., 2010, 18: 015012

DOI      URL     PMID      [本文引用: 1]

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Larsen P M, Schmidt S, Schiøtz J.

Robust structural identification via polyhedral template matching

[J]. Modell. Simul. Mater. Sci. Eng., 2016, 24: 055007

[本文引用: 1]

Hirth J P, Lothe J.

Theory of Dislocations

[M]. 2nd Ed., New York: John-Wiley, 1982: 73

[本文引用: 1]

Nabarro F R N.

Dislocations in a simple cubic lattice

[J]. Proc. Phys. Soc., 1947, 59: 256

DOI      URL     [本文引用: 1]

Kumar A, Morrow B M, McCabe R J, et al.

An atomic-scale modeling and experimental study of <c+a> dislocations in Mg

[J]. Mater. Sci. Eng., 2017, A695: 270

[本文引用: 2]

/