[gmx-users] strange new H-H bond formation during MD

[Mark Abraham]

Qiao Baofu wrote:
> Hi Mark,
> 
> Thanks for your reply.
> 
> I used these:
>   1. vmd em_out.gro 
>   2. use the "load data into molecules...", select md1.trr, and then load
>   3. when the anmination is finished, I can see some H-H bonds.

Right, so like I said earlier, you're not giving it your topology, 
because you're loading from a .gro file. Instead, VMD is making stuff 
up, because J. Random User would complain if it just showed some 
disconnected spheres that any chemist knows are bonded... You aren't 
making bonds. You can't make bonds in a normal MD simulation. What you 
are seeing is the consequence of VMD having to make stuff up, and if two 
hydrogens get close enough together, it'll figure they're bonded.

Mark