Gro文件

Files with the gro file extension contain a molecular structure in Gromos87 format. gro files can be used as trajectory by simply concatenating files. 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.

A sample piece is included below:

MD of 2 waters, t= 0.0
    6
    1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
    1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
    1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
    2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
    2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
    2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
   1.82060   1.82060   1.82060

Lines contain the following information (top to bottom):

• 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. 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):

• residue number (5 positions, integer). 残基序号，5位十进制数。
• residue name (5 characters). 残基名称，5位字符。
• atom name (5 characters). 原子名称，5位字符。
• atom number (5 positions, integer). 原子序号，5位十进制数。
• position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places). 原子坐标三列：x y z，8位十进制数包含3位小数。
• velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places). 速度，x y z 三列，8位十进制位包含4位小数。

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

<c>%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f</c>

• Fortran format

<fortran>(i5,2a5,i5,3f8.3,3f8.4)</fortran>

• 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.

分子坐标文件（.gro）。GROMACS的最主要分子坐标文件，明白这个文件，就基本明白使用GROMACS了。该文件类型的各个文本列字数固定，C语言的写入格式为： <c>%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f</c> 具体固定文本列有：残基序号，5位数；残基名称，5字母；原子名称，5字母；原子序号，5为数；原子坐标三列，X，Y，Z坐标各8位数，含3个小数位；速度同坐标，速度单位为nm/ps（km/s）。

参见

• Gromacs Manual