Bill and David,
Thank you for your replies. Your suggestion for extraction to a rst7 file
worked perfectly.
Jim Kress
-----Original Message-----
From: David A Case [mailto:david.case.rutgers.edu]
Sent: Thursday, November 16, 2017 10:21 PM
To: James Kress <jimkress_58.kressworks.org>
Cc: amber.ambermd.org
Subject: Re: How to extract one frame from a trajectory to use as input file
for new MD run?
On Thu, Nov 16, 2017, James Kress wrote:
> Is there some part of the Amber documentation that shows how to
> extract a single frame from a trajectory and then use that frame as
> the -c input for another, new MD run?
Use trajin to select the frame you want, e.g.
trajin myfile.nc 492 492 1
will select frame 492. Then use trajout to write this as a restart file:
trajout mynewfile.rst7 restart
This won't have velocities, so you will need to set ntx=1, irest=0, and use
tempi (for example) to choose random velocities appropriate for the
temerature you want.
> trajout frame1000.crd onlyframes 1000
This write the coordinates in "trajectory" format; you want them in
"restart"
format.
....dac
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Received on Fri Nov 17 2017 - 15:30:02 PST
