On Mon, Jan 22, 2018, Simon Kit Sang Chu wrote:
>
> I have my simulation completed and outputted the trajectory to mdcrd. I
> want to output several frames to inpcrd to restart another run. However,
> VMD does not seem to output the correct format and the VMD-outputted
> crd file is unreadable by AMBER.
>
> Is there anyone suggesting an alternative / a solution in VMD? I cannot
> imagine this has to be done by writing my own script.
Use cpptraj. Set trajin to your input trajectory (selecting the frames
you want), and trajout to an Amber restart file. Note that there are no
velocities in trajectory files, so you will probably want to set the tempi
variable on your subsequent MD to start from randomized velocities.
(Which format option did you use in VMD for attempting to write the restart
file?)
....dac
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Received on Mon Jan 22 2018 - 06:00:04 PST
