[Gonzalo Diaz Miron]

Hello, I’m new user of Genesis and I have some question, I was reading the manual and tutorials but I didn’t find the answers.

1. When I perform a restart of the dynamics, I know that the coordinates are read from the restart file and not from the pdb, but what about the velocities. This are read from the restart file too?, in this case the velocities are not setting randomly?, so temperature variable is used as a target temperature not for initial?
2. How can I see the structure from a restart file?
3. Finally, Is it possible to separate a long trajectory in the format dcd into differents frames in the format of rst ? How can I do that?.

Thank you so much for your attention, all the best.

[ckobayashi]

Hello,

 

1. If you set a restart file with the velocities in [INPUT],  the velocities are read from the file and temperature in [ENSEMBLE] is used as a target temperature. The restart file without the velocities is generated from minimization, and the other simulations will generate the restart file with velocities.
2. Please use rst_convert; https://www.r-ccs.riken.jp/labs/cbrt/samples/rst_convert/
3. No, we don’t have.

Sincerely yours,

 

Kobayashi

 

[Gonzalo Diaz Miron]

Thank you so much the answer!.