审稿人对Gromacs模拟提出意见，请求改正意见

zhufayan

各位老师，最近我发了一篇有关结合Gromacs研究液体结构的文章，审稿人对gromacs模拟部分提的意见很尖锐，但由于这是我的第一篇有关Gromacs的文章，有些意见我真不知道怎么改进，请各位老师指导改进谢谢。
审稿人给的意见如下：
I am unable to recommend the present work on"***" due to inconsistencyand inaccuracy. My major objections are : the DFT method with such a smallbasis set is not reliable at all and leads to erroneous claim（本工作中用的方法基组为ωB97XD functional[28] and the 6−311++G(d, p)）, similarly MDsimulation with such a small box is also not reliable （这个问题我可以解决）, the adopted method ispoor to describe the charge systems, the authors didn't analyze the energyoutput of MD simulations to understand the forces responsible for stability....
本工作中的计算模拟部分的计算方法叙述如下：
AllMD simulations were carried out using GROMACS-5.1.5 software package[27].The initial structure of NO3- was optimized at ωB97XD functional[28] and the 6−311++G(d, p) basis set level[29] in Gaussian16 package[30].The partial charges on each atom of NO3- were obtained from Ref. 31.The parameters of NO3- initially parametrized using AMBERwere converted to GROMACS format using the ACPYPE script[32]. Thewater molecules were modeled using the SPC/E model[33]. All bondsand angles of the water molecules were constrained using the SHAKE algorithm[34].Initially, energy minimization corrected atomic overlaps to ensure that themaximum force on any atom was below 100 kJ mol-1 nm-1 maintaininga pressure of 1 atm and a temperature of 300 K.
Allsystems were relaxed by an energy minimization step using the steepest descentmethod with a time step of 100 fs. Then, the equilibration in the isobaric-isothermal(NPT) ensemble was carried out for a 20 ns simulation length while maintainingthe pressure at 1 atm and temperature at 300 K using a velocity-rescalethermostat[35] and the Parrinello-Rahman scheme[36] witha time step of 1 fs. The production runs were carried out in the NPT ensemblefor 50 ns with a time step of 1 fs. The temperature was maintained using the V-rescalethermostat, while the pressure was controlled using the Parrinello-Rahmanbarostat. Long-range electrostatic interactions were guided by particle meshEwald (PME)[37-39] with a cut-off distance of4.7Å with a PME order of 6 and an Ewald tolerance of 10−6. Thetrajectory data were collected every 0.5 ps for analysis. Molecule visualizationwas displayed by the Visual Molecular Dynamics (VMD) program[40].The partial electric charge sets, Lennard-Jones parameters for the systems, andthe details of the simulation box are shown in the Supporting Information inTable S1 and S2.
恳请各位老师提供些改进的意见和方法，非常感谢

jimulation

这个DFT指的仅是优化NO3-的初始结构吗？这对于后续MD也没意义啊，分子结构是通过力场参数决定的。另外"partial electric charge sets"指的是原子电荷？不知这个和审稿人提出的"charge systems"有什么关联。

zhufayan

我是将NO3-结构优化后再将其用到GS中的.gro文件里（我没搞清楚您说的立场参数决定结构的事情），partial electric charge sets是原子电荷，这我是参考另一篇文献的。

jimulation

zhufayan 发表于 2020-12-25 11:38
我是将NO3-结构优化后再将其用到GS中的.gro文件里（我没搞清楚您说的立场参数决定结构的事情），partial el ...

跑MD时分子的结构并不会维持在你用量化计算得到的初始结构，而是会根据你的力场参数(top、itp中设定的键和非键参数)进行自动调整

zhufayan

老师，那您对我计算模拟的其他部分能不能指导下，或发下您的GS模拟计算的写作部分吧？谢谢

sobereva

能量极小化没有温度以及控压的概念，应当去maintaininga pressure of 1 atm and a temperature of 300 K.
能量极小化的步长也不是用时间来衡量的。前头已经说过了能量极小化了，没必要再写Allsystems were relaxed by an energy minimization step using the steepest descentmethod with a time step of 100 fs。

用ωB97XD/6-311++G**优化NO3-没有丝毫问题，审稿人要么不懂，要么瞎找碴。碰上个像样审稿人不会提出这个问题。

如果NO3-的电荷、bond和angle参数都是直接从别的地方获取的，那么优化NO3-这步完全多余。

你当前的描述并没有体现盒子怎么设的，没法回复你。

zhufayan

谢谢Sobereva老师的指导