Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line

From: Hugh Martin (
Date: Mon Mar 02 2009 - 10:42:53 CST

That's fantastic, a follow up question though: if I were to use your first
suggestion, would the constraint position in the second simulation start
precisely where it finished in the first simulation or would it be reset to
the SMD atom? There is some lag between the two in my simulations, stopping
and restarting periodically corrects this.

Many thanks,


2009/3/2 Peter Freddolino <>

> Hi Hugh,
> you shouldn't need to generate a new SMD.pdb file if you use an
> appropriate starting timestep for your subsequent simulations, which is
> a cleaner way to do things. You can read the last timestep from the
> restart xsc file:
> proc get_first_ts { xscfile } {
> set fd [open $xscfile r]
> gets $fd
> gets $fd
> gets $fd line
> set ts [lindex $line 0]
> close $fd
> return $ts
> }
> set currenttimestep [get_first_ts $inputname.xsc]
> firsttimestep $currenttimestep
> Alternatively, you can convert binary <-> ascii using catdcd:
> catdcd -o file.coor -otype namdbin file.pdb
> catdcd -o file.pdb -s file.psf -stype psf file.coor
> Finally, you need to use binaryrestart, not binaryoutput, to toggle
> ascii vs. binary restart files. binaryoutput only applied to the output
> files written if a run finishes completely.
> Best,
> Peter
> Hugh Martin wrote:
> > Hello,
> >
> > I'm attempting to automatically string together subsequent NAMD SMD
> > simulations via a script which detects when the previous simulation has
> > finished, converts and renames files to act as input files for the next
> > simulation, and then submits the job automatically. In order to do this
> > I need to convert the pdb output file from an initial simulation into an
> > SMD.pdb input file for a subsequent simulation (this would be done by a
> > trivial substitution of a field in the pdb output file). I only wish to
> > use an ASCII pdb file to refer namd to the SMD atom position; for the
> > coordinates, velocities and periodic boundaries I need to use binary
> > input files coor, vel, and xsc. Basically, I need both binary and ASCII
> > forms of output in order to link two SMD simulations automatically.
> >
> > This presents a problem, as by using binary input files, NAMD insists on
> > producing binary output files for restart files and final
> > coordinate/velocity files (circumventing fields such as "binaryoutput
> > off" in the .conf file). This makes direct conversion of the output
> > coordinate file to an ASCII SMD.pdb file non-trivial.
> >
> > Therefore, if my script, which links the first simulation to the
> > subsequent simulation, is going to succeed, I need NAMD to either output
> > in both binary and ASCII fomats (is this possible?), or I need to
> > convert the binary output into ASCII (.coor to .pdb) using the command
> > line (I know .coor files can be converted to .pdb files using vmd,
> > however scripted use of VMD windows on distant machines is not possible
> > to my knowledge).
> >
> > Any help or ideas would be greatly appreciated.
> >
> > Many thanks,
> >
> > Hugh

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