GROMACS格式的文件转成LAMMPS格式的工具GRO2LAM

sobereva

JMM上刚发表的GROMACS格式的文件转成LAMMPS格式的工具GRO2LAM

网址：
https://github.com/hernanchavezthielemann/GRO2LAM

原文：
From GROMACS to LAMMPS-GRO2LAM.pdf (3.29 MB, 下载次数 Times of downloads: 439)

2019-6-11 05:40 上传 Uploaded

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neocc

sobereva 发表于 2022-12-18 11:22
可以用InterMol

lammps 转 gromacs 还是有问题，会有如下报错：

intermol.exceptions.UnimplementedSetting: ['pair_style', 'none'] has not yet been implemented in InterMol for LAMMPS.

https://github.com/shirtsgroup/InterMol/issues/345
开发组好像没经费，摆烂了

neocc

打扰社长了，问题已解决，是anaconda的问题
删掉~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol*，下载最新的InterMol-0.1.2，解压进入InterMol-0.1.2文件夹后pip install .

neocc

sobereva 发表于 2022-12-18 11:22
可以用InterMol

社长，我试了最新的Intermol，测试gromacs的时候出现如下报错，会影响lmp2gmx转换嚒

1. INFO 2022-12-19 00:35:43 Converting dihedral1_vacuum
   
2. INFO 2022-12-19 00:35:43 Converting dihedral2_vacuum
   
3. INFO 2022-12-19 00:35:43 Converting dihedral3_vacuum
   
4. INFO 2022-12-19 00:35:43 Converting dihedral4_vacuum
   
5. INFO 2022-12-19 00:35:43 Converting dihedral5_vacuum
   
6. INFO 2022-12-19 00:35:43 Converting dihedral9_vacuum
   
7. Traceback (most recent call last):
   
8.   File "test_all.py", line 96, in <module>
   
9.     testing_function(args['compute_energies'], args['output_dir'])
   
10.   File "test_all.py", line 24, in test_gromacs_unit
    
11.     output_dir=output_dir)
    
12.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/tests/testing_tools.py", line 90, in convert_one_to_all
    
13.     output_dir=output_dir)
    
14.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/tests/testing_tools.py", line 219, in _convert_from_engine
    
15.     diff = convert.main(flags)
    
16.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/convert.py", line 223, in main
    
17.     system, prefix, gro_in, top_in = _load_gromacs(gromacs_files=args['gro_in'])
    
18.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/convert.py", line 573, in _load_gromacs
    
19.     system = gmx.load(top_in, gro_in)
    
20.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 38, in load
    
21.     return parser.read()
    
22.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 416, in read
    
23.     self.process_file(self.top_filename)
    
24.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1142, in process_file
    
25.     self.process_line(top_filename, '{0} {1}'.format(append, line))
    
26.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1281, in process_line
    
27.     self.process_dihedraltype(line)
    
28.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1487, in process_dihedraltype
    
29.     self.gromacs_dihedral_types, self.canonical_dihedral)
    
30.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 1509, in process_forcetype
    
31.     kwds = self.create_kwds_from_entries(fields, gromacs_force_type, offset=n_atoms+1)
    
32.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/gromacs/gromacs_parser.py", line 347, in create_kwds_from_entries
    
33.     entries, force_class, offset=offset)
    
34.   File "~/anaconda3/envs/vaspkit/lib/python3.6/site-packages/intermol/forces/forcefunctions.py", line 139, in create_kwds_from_entries
    
35.     kwds[p] = float(entries[offset+i]) * u[i]
    
36. IndexError: list index out of range

复制代码

sobereva

neocc 发表于 2022-12-15 16:41
请问楼主有lammps2gromacs的转换工具嚒

可以用InterMol

neocc

请问楼主有lammps2gromacs的转换工具嚒

bobosiji

如果某人只会gmx，但想用lammps里面的力场，请问这个工具有用么？
粗看了下jmm的原文，以及github里的说明。似乎该工具支持的力场其实都是gmx能用的，，，
如果力场用gmx就能跑的话，把输入文件转成lammps有何意义呢。。。

huangjin

太好了，谢谢分享！

tjuptz

请问有大佬测试或使用过这个工具吗，可靠性如何呢？

diaok

曾经打算自己开坑写一个，但是python学的太渣没法保证各种兼容性，只在自己勉强能用的阶段

少年爱吃地三鲜

真的太好了！收藏！