Gmx trjconv 2019

2019-12-24: fix bug for small time step: 2019-12-10: fix bug for OPLS force field: 2019-11-17: fix bug for c6, c12 of old version tpr: 2019-11-06: apbs FILE.apbs &> FILE.out: on ubuntu 18.04 may not work, then delete & 2019-11-03: fix bug for time stamp: 2019-09-19: push to gmxtool DESCRIPTION¶ gmx spatial calculates the spatial distribution function and outputs it in a form that can be read by VMD as Gaussian98 cube format. For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated in about 30 minutes, with most of the time dedicated to the two runs through trjconv that are required to center everything properly.2019年4月25日追記: 一部の記述を修正。 目的 GromacsのMD計算で得られたトラジェクトリファイルを適切に変換し、VMDやPyMOLなどで表示するための知識やメモ。 特にgmx trjconvコマンド周辺を使った... gmx-dos(1) Analyze density of states and properties based on that gmx-dyecoupl(1) Extract dye dynamics from trajectories gmx-principal(1) Calculate principal axes of inertia for a group of atoms gmx-tcaf(1) Calculate viscosities of liquids gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from trajectories gmx-vanhove(1)

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VMD/QwikMD/NAMD 1. Visual Molecular Dynamics (VMD) is a graphical program for MD simulations. Due to the graphical user interface it was quite easy to run the first MD after a short orientation.

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First release: 2019-Jan-2 Last update: 2020-Jan-6. ... 对复杂的分子, 去除周期性的子程序可能会崩溃, 在这种情况下你可以使用gmx trjconv.


gmx trjconv -f cent.gro -s md.tpr -fit rot+trans -o fit.gro 当然分析作业远远不止观察分子运动那么简单,还可以调用各种脚本考察希望的量,这里暂不讨论。 编辑于 2019-04-03 gmx cluster~gmx rms~gmx gyrate~gmx energy~gmx trjconv~gmx trjconv~gmx trjconv~gmx trjconv~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj ...

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