在使用Gromacs进行分子动力学模拟的时候，首先一步是将从氨基酸数据库下载得到的PDB文件处理为Gromacs所使用gro文件，使用pdb2gmx可以做到这一点。
pdb2gmx命令的使用时有很多参数，需要细心设定。比如：
1、若希望多肽两端闭合为NH2和COOH，需要在命令后面加上-ter参数，命令执行后会出现选择项，此时可以手动选择多肽两端闭合选项；
#The protonation state of N- and C-termini can be chosen interactively with the -ter flag. Default termini are ionized (NH3+ and COO-), respectively. Some force fields support zwitterionic forms for chains of one residue, but for polypeptides these options should NOT be selected. The AMBER force fields have unique forms for the terminal residues, and these are incompatible with the -ter mechanism. You need to prefix your N- or C-terminal residue names with "N" or "C" respectively to use these forms, making sure you preserve the format of the coordinate file. Alternatively, use named terminating residues (e.g. ACE, NME).
2、若residues中包括LYS, ASP, GLU, CYS or HIS等氨基酸（amino acid)，可以选择单独处理，以确定这几个氨基酸末参与缩合的N的存在方式（NH2或NH3+）。
The program has limited intelligence, it reads a number of database files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.), if necessary this can be done manually. The program can prompt the user to select which kind of LYS, ASP, GLU, CYS or HIS residue is desired. For Lys the choice is between neutral (two protons on NZ) or protonated (three protons, default), for Asp and Glu unprotonated (default) or protonated, for His the proton can be either on ND1, on NE2 or on both. By default these selections are done automatically. For His, this is based on an optimal hydrogen bonding conformation. Hydrogen bonds are defined based on a simple geometric criterion, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively.
3、可以使用-ignh忽略原pdb文件所带氢，而按照Gromacs的方式产生新的氢键。
具体使用方式需要根据研究方向确定。如果只是想研究多肽脱水缩合的动力学情况，可以全部选择为NH2、COOH以闭合residue；如果研究包含LYS, ASP, GLU, CYS or HIS等氨基酸的residue内部是否存在Cross-Link，则可以选择NH3+，COO-为端。