On Fri, Oct 14, 2011 at 8:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > The crd file (mdcrd, amber trajectory, written at intervals specified by
> > ntwx) doesn't contain velocities, unless you specifically specify this by
> > setting ntwv=1.
>
> That causes the velocities to be written to the mdvel file.
> But I doubt ptraj knows how to combine mdcrd+mdvel to produce
> restrts (since mdvel writing is unusual).
>
There's an option now to write an mdcrd file that has combined coordinates
and velocities in the same NetCDF trajectory. Only cpptraj can process this
to provide a velocity-containing restart file from a specific snapshot as
far as I know (or is this not in a released cpptraj version? Dan would
know).
>
> Beyond that, both mdcrd and mdvel have less precision than restrt,
> so even if you had both and combined them to produce a restrt, it
> wouldn't be as good as a normal restrt, and some equilibration
> could be desireable.
>
Actually if they use NetCDF (which everybody should be, and the only option
for combining mdvel/mdcrd), then they have more precision than a restart
(full single precision, unformatted), so this would be unnecessary.
All the best,
Jason
> Bill
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 14 2011 - 21:00:03 PDT
