AW: memory-optimized version binary coordinates?

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 21 2012 - 00:39:57 CDT

I guess you can do that while loading the pdb into vmd and save coordinates
as binpdb. Than of course use bincoordinates in the configuration file.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Carlos Sosa
Gesendet: Sonntag, 17. Juni 2012 18:25
An: Aron Broom
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: memory-optimized version binary coordinates?

 

Yes, exactly. I need to generate that bin file. Similar to the compressed
psf which is triggered by "genCompressedPsf on". The wiki is a little
obscure as to how to generate the pdb file that appears to be needed.

On Sun, Jun 17, 2012 at 11:10 AM, Aron Broom <broomsday_at_gmail.com> wrote:

I see, I don't know anything about compressed psf, so I can't help out with
that aspect.

What I don't understand from this is:

bincoordinates apoa1-out.coor
outname ./apoa1-out.coor

you realize that bincoordinates is the input? Your file seems a bit
cyclical.

 

On Sun, Jun 17, 2012 at 11:20 AM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:

This file produces apoa1.psf.inter apoa1.psf.inter.bin only. Did I miss to
add anything else?

cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0

coordinates apoa1.pdb
bincoordinates apoa1-out.coor
temperature 300
seed 74269

genCompressedPsf on

switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20

PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80

structure apoa1.psf

parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0

timestep 1.0
fullElectFrequency 4

numsteps 500
outputtiming 20

outputname ./apoa1-out

binaryoutput yes

On Sat, Jun 16, 2012 at 9:22 PM, Aron Broom <broomsday_at_gmail.com> wrote:

I doubt that apoa1.pdb file is in binary, it is probably ASCII.

When you say "binaryoutput yes" you just mean that you want the
apoa1-out.coor file to be in binary rather than ASCII, but it doesn't affect
what you supply as the input for that run.

So, if you only have a PDB file for input, you should say "binaryoutput
yes", but then just have "coordinates apoa1.pdb". If you later want to use
the output from that run, then you will provide the new coordinates as:

"coordinates apoa1.pdb"
"bincoordinates apoa1-out.coor"

In this way the binary coordinates are used, but the ASCII coordinate file
is still required to assign the atoms or something of that sort, even though
the positions are ignored.

~Aron

 

On Sat, Jun 16, 2012 at 8:33 PM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:

Aaron,

I used this option but when I run the mem optimized version I get this
error... Also, I did not see any difference in the apoa1.pdb file before
and after generating the compressed psf file.

Info: Running with 1 output processors (1 of them will output
simultaneously).
FATAL ERROR: Incorrect atom count in binary file ./apoa1.pdb
CmiAbort is calling on PE:0
aborting job:
FATAL ERROR: Incorrect atom count in binary file ./apoa1.pdb

configuration file:
cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0

bincoordinates apoa1.pdb
temperature 300
seed 74269

useCompressedPsf on
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20

PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80

structure apoa1.psf.inter
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0

timestep 1.0
fullElectFrequency 4

numsteps 500
outputtiming 20

outputname ./apoa1-out

On Fri, Jun 15, 2012 at 4:18 PM, Aron Broom <broomsday_at_gmail.com> wrote:

when you do a run, have:

binaryoutput yes

in the config file.

Then your coor, vel, and dcd files will be binary.

 

On Fri, Jun 15, 2012 at 4:43 PM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:

Hello,

Any information on how to obtain binary format representation for the
coordinates?

>From the NAMD wiki:

III. obtain a binary format representation of your coordinates. The
coordinate output file of a non memory optimized run would work. Or extract
the binary coordinates using VMD.

IV. replace "coordinates" with "bincoordinates" and replace the reference to
the pdb file with a file containing binary format coordinates.

Thanks

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
-- 
Carlos P Sosa, Ph.D.
Computational Chemistry Consultant and Adjunct Assistant Professor
Biomedical Informatics and Computational Biology (BICB) 
Minnesota Supercomputing Institute for Advanced Computational Research,
University of Minnesota, Walters Library # 509, 117 Pleasant Street,
Minneapolis, MN 55455.
-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
-- 
Carlos P Sosa, Ph.D.
Computational Chemistry Consultant and Adjunct Assistant Professor
Biomedical Informatics and Computational Biology (BICB) 
Minnesota Supercomputing Institute for Advanced Computational Research,
University of Minnesota, Walters Library # 509, 117 Pleasant Street,
Minneapolis, MN 55455.

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