[gmx-users] a question about pepetide chains interaction

[leafyoung81-group at yahoo.com]

"generate the structure with two pepetides in one file and name each with different identifier"

I am not clear about this. Generate one topologies or one .gro file?

As long as, in [ molecules ] sections, there are separated entry to each chain, it is fine.

Yang Ye

Wang Zhun <wangzhun at pumc.edu.cn> wrote: Hi, all,

If I want to simulate the interaction between two peptides, based on previous mailling posts, I should generate two separate .gro structures and .top topologies for each pepetide and combine them for further MD simulation.
Now I wonder if I generate the structure with two pepetides in one file and name each with different identifier, can I carry MD simulation in a way of simulation of protein with multiple subunits in the FAQ?

Thanks!
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