Thanks Bill,
After I sent the first email, I remembered that it is possible to dump
multiple restrt files as you mentioned; just add a minus sign to the
argument of ntwr, e.g. ntwr = -1000. I thought of doing that, although it
is not as clean as having all the frames saved in a single trajectory file.
But having a hundred restrt files with the velocities output automatically
sounds much more preferable than having to manually compose the restrts
with the velocities. Is there any talk of making the following workflow,
umm, work?
1. save coords and velocities both in the same netcdf file with the mdin
options "ioutfm = 1, ntwv = -1, ntwx = 100"
2. to subsequently print out individual restart frames (with
velocities), just give ptraj the following commands:
trajin mdcrd
trajout <framename> restart
go
It seems like this should be a standard workflow, rather than having to
deal with the other workarounds each of us has suggested. Thanks for the
help.
Sid
On Tue, Jan 24, 2012 at 4:29 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> To get velocities to match mdcrd, you need to save mdvel as well,
> then manually compose restrts from corresponding frames of mdcrd/mdvel.
> Note that these will truncate precision so won't be as fully equilibrated
> as the trajectories they came from. This is true to a lesser degree for
> non-netcdf restrts, since they have less precision than the binary
> format.
>
> Once upon a time there was talk of an option to dump multiple restrt
> files during the trajectory, not sure what the status of that is.
>
> Bill
>
> Sidney Elmer <paulymer.gmail.com> wrote:
>
> > Hi,
> >
> > I set up my simulation with the following flags: ioutfm = 1, ntwv = -1,
> > with the expectation that I would be able to pull restart files from any
> of
> > the frames saved in the mdcrd file. However, when I output the frames
> into
> > individual restart files using ptraj:
> >
> > trajin mdcrd
> > trajout frame restart
> > go
> >
> >
> > all of the velocities are 0.000000. Did I do something wrong? How do I
> > get the restart files with the velocities as I was expecting? Thanks for
> > your help.
> >
> > Sid
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Received on Tue Jan 24 2012 - 17:30:02 PST
