Hi,
On Tue, May 20, 2014 at 9:05 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> Firstly I'd like to know about possibility to generate *.rest file
> (consisted of coordinates +felicitates +box vectors in specified time step)
> from selected step of the output trajectory or md.out file. For instance
> one of my recent simulations have been crashed and broken check point file
> have been created so I'd like to restore it manually.
You can restore coordinates from a trajectory file, e.g.
trajin input.nc 30 30 # selects frame 30 only
trajout restart.rst7
but unless you were also writing velocities (i.e. ntwv != 0) you
cannot create a true restart file. If you have a separate velocity
trajectory you can use those velocities with the 'mdvel' keyword, e.g.
trajin input.nc 30 30 mdvel vel.nc
or if you wrote a combined coordinate/velocity trajectory (NetCDF
only) the velocities will be read in automatically.
You can generate random starting velocities for a new MD run according
to a temperature distribution by running with irest=0, ntx=1, and
ig=-1.
Hope this helps,
-Dan
>
> James
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 20 2014 - 09:00:04 PDT
