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
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