Gromacs文件格式(1)

1. File formats
   edi
   Files with the edi file extension contain information for gmx mdrun to run Molecular Dynamics with Essential Dynamics constraints.
   具有edi文件扩展名的文件包含gmx-mdrun在基本动力学约束下运行分子动力学的信息

edr
The edr file extension stands for portable energy file. The energies are stored using the xdr protocol.
See also gmx energy.

ene
The ene file extension stands for binary energy file. It holds the energies as generated during your gmx mdrun.
The file can be transformed to a portable energy file (portable across hardware platforms), the edr file using the program gmx eneconv.
See also gmx energy.

gro
Files with the gro file extension contain a molecular structure in Gromos87 format.
具有gro文件扩展名的文件包含Gromos87格式的分子结构
gro files can be used as trajectory by simply concatenating files.
gro文件可以通过简单地连接文件来用作轨迹
An attempt will be made to read a time value from the title string in each frame, which should be preceded by ‘t=‘, as in the sample below.
将尝试从每帧的标题字符串中读取一个时间值，该时间值之前应加上“t=”，如下面的示例所示

Lines contain the following information (top to bottom):
行包含以下信息（从上到下）：
title string (free format string, optional time in ps after ‘t=’)
number of atoms (free format integer)
one line for each atom (fixed format, see below)
box vectors (free format, space separated reals), values: v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y), the last 6 values may be omitted (they will be set to zero). GROMACS only supports boxes with v1(y)=v1(z)=v2(z)=0.
This format is fixed, ie. all columns are in a fixed position.
这种格式是固定的，即所有列都位于固定的位置。
Optionally (for now only yet with trjconv) you can write gro files with any number of decimal places, the format will then be n+5 positions with n decimal places (n+1 for velocities) in stead of 8 with 3 (with 4 for velocities). Upon reading, the precision will be inferred from the distance between the decimal points (which will be n+5). Columns contain the following information (from left to right):
可选地（目前仅适用于trjconv），您可以使用任意数量的小数位编写gro文件，格式将为n+5个位置，带有n个小数位（速度的n+1个小数位），而不是8个位置，带有3个小数位（速度带有4个小数位）。在读取时，精度将从小数点之间的距离推断出来（这将是n+5）。列包含以下信息（从左到右）：???
residue number (5 positions, integer)
residue name (5 characters)
atom name (5 characters)
atom number (5 positions, integer)
position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places)
velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places)
Note that separate molecules or ions (e.g. water or Cl-) are regarded as residues. If you want to write such a file in your own program without using the GROMACS libraries you can use the following formats:
C format
“%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f”
Fortran format
(i5,2a5,i5,3f8.3,3f8.4)
Pascal format
This is left as an exercise for the user
Note that this is the format for writing, as in the above example fields may be written without spaces, and therefore can not be read with the same format statement in C.

hdb
The hdb file extension stands for hydrogen database Such a file is needed by gmx pdb2gmx when building hydrogen atoms that were either originally missing, or that were removed with -ignh.
itp
The itp file extension stands for include topology. These files are included in topology files (with the top extension).
log
Logfiles are generated by some GROMACS programs and are usually in human-readable format. Use more logfile.

map
This file maps matrix data to RGB values which is used by the gmx do_dssp program.
此文件将矩阵数据映射到gmx do_dssp程序使用的RGB值
The format of this file is as follow: first line number of elements in the colormap. Then for each line: The first character is a code for the secondary structure type. Then comes a string for use in the legend of the plot and then the R (red) G (green) and B (blue) values.
In this case the colors are (in order of appearance): white, red, black, cyan, yellow, blue, magenta, orange.

mdp
See the user guide for a detailed description of the options.
Below is a sample mdp file. The ordering of the items is not important, but if you enter the same thing twice, the last is used (gmx grompp gives you a note when overriding values).
但是，如果您输入两次相同的内容，就会使用最后一个（gmx-grompp在重写值时会给您一个提示）
Dashes and underscores on the left hand side are ignored.
忽略左侧的虚线和下划线
The values of the options are values for a 1 nanosecond MD run of a protein in a box of water.
Note: The parameters chosen (e.g., short-range cutoffs) depend on the force field being used.

ndx

The GROMACS index file (usually called index.ndx) contains some user definable sets of atoms. The file can be read by most analysis programs, by the graphics program (gmx view) and by the preprocessor (gmx grompp). Most of these programs create default index groups when no index file is supplied, so you only need to make an index file when you need special groups.
First the group name is written between square brackets. The following atom numbers may be spread out over as many lines as you like. The atom numbering starts at 1.

rtp
The rtp file extension stands for residue topology.
rtp文件扩展名代表残基拓扑
Such a file is needed by gmx pdb2gmx to make a GROMACS topology for a protein contained in a pdb file.
gmx pdb2gmx需要这样一个文件来为pdb文件中包含的蛋白质创建GROMACS拓扑
The file contains the default interaction type for the 4 bonded interactions and residue entries, which consist of atoms and optionally bonds, angles dihedrals and impropers.
该文件包含了4个键合相互作用和残基条目的默认相互作用类型，这些条目包括原子和可选的键、角、二面角和非常规键。
Parameters can be added to bonds, angles, dihedrals and impropers, these parameters override the standard parameters in the itp files.
可以向键、角、二面角和非常规键添加参数，这些参数将覆盖itp文件中的标准参数。
This should only be used in special cases.
这只能在特殊情况下使用。
Instead of parameters a string can be added for each bonded interaction, the string is copied to the top file, this is used for the GROMOS96 forcefield.
对于每个键合相互作用，可以添加一个字符串而不是参数，该字符串会被复制到顶部文件中，这用于GROMOS96力场。
gmx pdb2gmx automatically generates all angles, this means that the [angles] field is only useful for overriding itp parameters.
gmx pdb2gmx会自动生成所有角度，这意味着[angles]字段只用于覆盖itp文件中的参数。
gmx pdb2gmx automatically generates one proper dihedral for every rotatable bond, preferably on heavy atoms.
gmx pdb2gmx会自动生成每个可转动键的一个适当的二面角，最好在重原子上。
When the [dihedrals] field is used, no other dihedrals will be generated for the bonds corresponding to the specified dihedrals.
当使用[dihedrals]字段时，将不会为与指定二面角相对应的键生成其他二面角。
It is possible to put more than one dihedral on a rotatable bond.
可以在一个可转动键上设置多个二面角。
gmx pdb2gmx sets the number exclusions to 3, which means that interactions between atoms connected by at most 3 bonds are excluded.
gmx pdb2gmx将排除数设置为3，这意味着将排除通过最多3个键相连接的原子之间的相互作用。
Pair interactions are generated for all pairs of atoms which are separated by 3 bonds (except pairs of hydrogens).
会为通过3个键相连的所有原子对（除了氢原子对）生成成对相互作用。
When more interactions need to be excluded, or some pair interactions should not be generated, an [exclusions] field can be added, followed by pairs of atom names on separate lines.
当需要排除更多相互作用，或者不希望生成某些原子对之间的相互作用时，可以添加一个[exclusions]字段，然后是分别位于单独行上的原子名称对。
All non-bonded and pair interactions between these atoms will be excluded.
所有这些原子之间的非键合和成对相互作用都将被排除。
A sample is included below.

top
The top file extension stands for topology. It is an ascii file which is read by gmx grompp which processes it and creates a binary topology (tpr file).
A sample file is included below:

tpr
The tpr file extension stands for portable binary run input file. This file contains the starting structure of your simulation, the molecular topology and all the simulation parameters. Because this file is in binary format it cannot be read with a normal editor. To read a portable binary run input file type:

gmx dump -s topol.tpr

or if you’re not such a fast reader:

gmx dump -s topol.tpr | less

You can also compare two tpr files using:

gmx check -s1 top1 -s2 top2 | less

trr
Files with the trr file extension contain the trajectory of a simulation. In this file all the coordinates, velocities, forces and energies are printed as you told GROMACS in your mdp file. This file is in portable binary format and can be read with gmx dump:

gmx dump -f traj.trr

or if you’re not such a fast reader:

gmx dump -f traj.trr | less

You can also get a quick look in the contents of the file (number of frames etc.) using:

gmx check -f traj.trr

xtc
The xtc format is a portable format for trajectories.
XTC格式是用于轨迹的一种可移植格式。
It uses the xdr routines for writing and reading data which was created for the Unix NFS system.
它使用为Unix NFS系统创建的xdr例程来进行数据的写入和读取。
The trajectories are written using a reduced precision algorithm which works in the following way:
轨迹是使用一种降低精度的算法进行写入，其工作方式如下：
the coordinates (in nm) are multiplied by a scale factor, typically 1000, so that you have coordinates in pm.
坐标（以纳米为单位）乘以一个缩放因子，通常为1000，以得到以皮米为单位的坐标。
These are rounded to integer values. 这些值被四舍五入为整数。
Then several other tricks are performed, for instance making use of the fact that atoms close in sequence are usually close in space too (e.g. a water molecule).
然后执行几个其他技巧，例如利用原子在序列中紧邻通常也在空间中紧邻的事实（例如水分子）。
To this end, the xdr library is extended with a special routine to write 3-D float coordinates.
为此，xdr库被扩展，增加了一个特殊的例程用于写入3D浮点坐标。
All the data is stored using calls to xdr routines.所有的数据都是使用xdr例程的调用进行存储的。
int magic
A magic number, for the current file version its value is 1995.一个魔数，对于当前文件版本，其值为1995。
int natoms
The number of atoms in the trajectory.轨迹中的原子数。
int step
The simulation step.
float time
The simulation time.
float box[3][3]
The computational box which is stored as a set of three basis vectors, to allow for triclinic PBC. For a rectangular box the box edges are stored on the diagonal of the matrix.
计算盒子，以一组三个基向量的形式存储，以允许三斜晶体周期性边界条件。对于矩形盒子，盒子边缘存储在矩阵的对角线上。
3dfcoord x[natoms]
The coordinates themselves stored in reduced precision. Please note that when the number of atoms is smaller than 9 no reduced precision is used.
坐标本身以降低的精度存储。请注意，当原子数小于9时，不使用降低的精度。

xvg
Almost all output from GROMACS analysis tools is ready as input for Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also free software. It produces PostScript? output, which is very suitable for inclusion in eg. LaTeX documents, but also for other word processors.
GROMACS分析工具的几乎所有输出都可以作为Grace（以前称为Xmgr）的输入。我们使用Grace，因为它非常灵活，而且它也是免费软件。它生成PostScript?输出，非常适合包含在例如LaTeX文档中，也适用于其他文字处理软件。
A sample Grace session with GROMACS data is shown below: