[gmx-users] Error in Energy Minimization

[Mark Abraham]

Sunny wrote:
> Hi,
> 
> Continue to the energy minimization problem. I use l-bfgs to run the 
> energy minimization for the structure summarized in the previous message 
> below. The em output topology confout.gro doesn't contain velocity data. 
> Then, I try to convert confout.gro into .pdb format by:

As Tsjerk said, EM output doesn't have velocities because you aren't 
doing a simulation. If you want a pdb file as output from mdrun, then 
using the -c file.pdb flag to mdrun is the way to go, rather than 
converting after the fact.

Mark