From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Mar 07 2014 - 01:40:25 CST
Yes, if you set "binaryrestart no" and "binaryoutput no" the vel and coor files will have pdb format. The dcd is always binary.
> -----Ursprüngliche Nachricht-----
> Von: Hassan Kianinejad [mailto:hasan_at_cs.ucla.edu]
> Gesendet: Freitag, 7. März 2014 00:38
> An: Norman Geist
> Betreff: Re: AW: namd-l: benchmark info
> Thank you so much for your illustration. But when I look at the output
> files generated, (.vel, .coor etc) they are not readable. Actually I am
> using NAMD-Lite now to do some profiling.
> Kind regards,
> Hassan Kianinejad
> Graduate Student
> VLSI CAD Lab, UCLA
> ----- Original Message -----
> From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
> To: "Hassan Kianinejad" <hasan_at_cs.ucla.edu>
> Cc: "Namd Mailing List" <namd-l_at_ks.uiuc.edu>
> Sent: Thursday, February 27, 2014 11:18:46 PM
> Subject: AW: namd-l: benchmark info
> If you take the namd manual and lookup the commands in the apoa1 config
> file, you might figure out most of your questions. Usually the PDB
> holds the initial coordinates and some naming of atoms. In addition the
> PSF (if charmm FF is used) file will hold the
> atom/bind/angle/dihedral/.... parameters. Initial velocities are
> introduced randomly by the "temperature" keyword. Please notice that
> the "result" of a md simulation is _NOT_ _ONE_ set of new coordinates
> but a "trajectory" (DCD file) that can be analyzed afterwards. During
> simulation, restart information gets written to
> restartname.xsc/coor/vel if set, or othwerwise
> *.xsc -> Box size
> *.coor -> Coordinates
> *.vel -> Velocities
> *.dcd -> Trajectory
> Additionally, one redirectes namds stdout to a logfile holding the
> energies and timing information. Please be aware that doing comparison
> benchmarks should come with some experience on both codes in case of
> getting the best performance configured out of them to be truly fair.
> Additionally, as initial movements are introduced randomly you will
> usually not be able to reproduce a trajectory, this has nothing to do
> with precision. Also, if using parallelization, you will not be able
> reproduce the same energies/coordinates even with one code, starting
> with the same velocities. So you need to carefully describe your metric
> of "precision".
> Norman Geist.
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Hassan Kianinejad
> > Gesendet: Donnerstag, 27. Februar 2014 23:34
> > An: namd-l_at_ks.uiuc.edu
> > Betreff: namd-l: benchmark info
> > Hi
> > I am a graduate student researcher at UCLA Computer Science
> > and I have some questions about input and output files for testing
> > source code.
> > I downloaded this benchmark: apoa1 and in this directory I looked at
> > some of the files; however I did not quite figure out which file
> > contains atom's info (like position; initial velocity; type; etc).
> > also what is included in the simulation output file? (should be final
> > positions and velocity of all atoms, right?)
> > Because I need to run my own source code to do the simulation
> > sequentially and compare my own results to look for
> > difference/precision.
> > I would really appreciate it if you could guide me through this
> > process.
> > Kind regards,
> > Hassan Kianinejad
> > Graduate Student
> > VLSI CAD Lab, UCLA
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