[gmx-users] creation coordinate file with special distance between system components

Atila Petrosian atila.petrosian at gmail.com
Wed Mar 19 09:03:27 CET 2014

Dear all

My system contains protein and ligand. I know if I do MD simulation,
distance between protein and ligand will change. I want to have some
coordinate files (gro file) such that in each of coordinate files, distance
between protein and ligand be a special value.

For example,

coordination file number                 distance
------------------------------                 -----------
1                                                    0.05
2                                                    0.1
3                                                    0.15
4                                                    0.2
98                                                  4.9
99                                                  4.95
100                                                5

Is there a tool in gromacs which do this issue?

I do not like use pull code.

Any help will highly appreciated.

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