From: Richard Law (rlaw_at_hanyou.llnl.gov)
Date: Tue Oct 25 2005 - 15:44:17 CDT
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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