Note there is also a command in cpptraj called 'setvelocity' that can
be used to set random velocities at a specified temperature. The
GitHub version includes options which will adjust velocities taking
into account constraints, as well as an option to zero momentum.
-Dan
On Thu, Nov 16, 2017 at 10:20 PM, David A Case <david.case.rutgers.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Nov 20 2017 - 08:30:05 PST
