Re: memory-optimized version binary coordinates?

From: Carlos Sosa (sosa0006_at_r.umn.edu)
Date: Mon Jun 25 2012 - 15:06:19 CDT

Norman,

Thanks. For those of us that do not use VMD, Here is Jim Phillips'
suggestion:

You can use the psfgen binary included with NAMD for this, with the
following commands:

readmol psf apoa1.psf pdb apoa1.pdb

writemol namdbin apoa1.coor

I tested this and now it is working.

I think that the wiki should be updated with your info (they mention VMD)
and Jim's suggestion.

On Thu, Jun 21, 2012 at 12:39 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> 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.****
>

-- 
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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