[gmx-users] How to create correct .gro file?

[Mark Abraham]

> Dear friends,
>
> I'm trying to create a .gro file by myself with a C++
> program. I created a file with the following format:
> "%5d%5s%5s%5d%8.3lf%8.3lf%8.3lf"
> and at the end, I put a line containing the components
> of the box vectors (with the exact order that it
> should be).
> But, when I used VMD to visualize my new .gro file, it
> didn't show me anything, and there appeared some
> messages on VMD console like this:
>
> Info) Using plugin gro for structure file basin1_t.gro
> Warning, error reading box, unexpected end-of-file
> reached

Bingo... "unexpected end of file". The .gro format requires the first few
lines to be a title and a number of atoms. If you omit these, then some
readers will blindly make the best of what *is* on those two lines and
then carry on with attempting to read the file. Go and look at some real
.gro files and copy their format more closely.

Mark