From: Carlos Sosa (sosa0006_at_r.umn.edu)
Date: Sat Jun 16 2012 - 19:33:36 CDT
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
>
>
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