Re: memory-optimized version binary coordinates?

From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Jun 17 2012 - 11:34:48 CDT

Hmmm, I don't I understand what you are trying to do. You already have a
psf and a coordinate file (pdb or something) and for whatever reason, you
want to convert those to a compressed psf and a binary coordinate file?

I don't understand about needing to generate the pdb, you don't already
have a pdb? What do you have for coordinates at the moment?

I'm not sure about the wiki as I've never looked at it, but I highly
recommend the NAMD 2.9 user guide, it is quite well documented.

On Sun, Jun 17, 2012 at 12:24 PM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:

> 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.
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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