From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Oct 25 2005 - 16:11:44 CDT
Thank you for that tip.
Now, how do I get NAMD to write out the text from a
dynamics run, as I wish to know which frame in a
trajectory is the lowest in energy.
Richard
--- Richard Law <rlaw_at_hanyou.llnl.gov> wrote:
>
> If your .coor is in binary then you have
> binaryoutput set to "yes". You
> need to change that. (to "no".)
>
> Rich.
>
>
> On Tue, 25 Oct 2005, Richard Wood wrote:
>
> > Hi all,
> >
> > How does on save the resulting coordinates of a
> NAMD
> > minimization in a format to do dynamics?
> >
> > I have a starting PDB and I want to run 1000 steps
> of
> > minimization, save it to a second PDB file and
> then
> > run dynamics.
> >
> > It says in the NAMD manual to use:
> >
> > "outputname < output PDB file >
> >
> > Acceptable Values: UNIX filename prefix
> >
> > Description: At the end of every simulation, NAMD
> > writes two PDB files, one containing
> > the final coordinates and another containing the
> final
> > velocities of all atoms in the simulation.
> > This option specifies the file prefix for these
> two
> > files. The position coordinates will be saved
> > to a file named as this prefix with .coor
> appended.
> > The velocities will be saved to a file named
> > as this prefix with .vel appended. For example, if
> the
> > prefix specified using this option was
> > /tmp/output, then the two files would be
> > /tmp/output.coor and /tmp/output.vel."
> >
> > However, .coor files are binary files.
> >
> > So how do I obtain the coordinates?
> >
> > Richard
> >
> >
> >
> > __________________________________
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> >
>
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