On Thursday, August 25, 2016, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Thanks, that worked. A nice option might be to have cpptraj detect NaN's
> and stop reading. :-)
You can use the 'check' command with the 'skipbadframes' option to get
something like this behavior - see the manual for details.
-Dan
>
> The interesting result is that I can't just scale selected atoms'
> velocities up to impart user 'taps' to my molecule, since the
> reinforcement of modes seems to be causing blowup, rather than
> collisions. Adding an orthogonal velocity component may work better.
>
> Bill
>
>
>
> On 8/25/16 1:47 PM, Hai Nguyen wrote:
> > may be you can use cpptraj to compute the center of mass (or anything
> else)
> > of your trajectory, plot the output to see the messed up frames?
> >
> > If you know specific frame, you can specify *trajin my.mdcd 1
> > your_given_frame*?
> >
> > Hopefully I understand your question correctly.
> >
> > Hai
> >
> > On Thu, Aug 25, 2016 at 4:26 PM, Bill Ross <ross.cgl.ucsf.edu
> <javascript:;>> wrote:
> >
> >> I have a netcdf mdcrd file in which the energies went south due to my
> >> user interactivity feature.
> >>
> >> When I try to load the mdcrd in VMD, nothing happens except this
> >> informative console message:
> >>
> >> Info) Using plugin crd for coordinates from file
> >> amber14/proj/cat_md62.crd
> >> Problem reading CRD file
> >> Info) Finished with coordinate file amber14/proj/cat_md62.crd.
> >>
> >> I'd like to watch how the blowup occurred - is there some way to repair
> >> the netcdf up to that point, so I can watch what happens?
> >>
> >> Thanks,
> >>
> >> Bill
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <javascript:;>
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 25 2016 - 17:00:02 PDT
