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mittko Offline OP
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I have tried to find what the numbers in the header of a restart file exactly represent (especially the CRYSTAL parameters), but was not able to find this info anywhere. Do you know what the values below the CRYSTAL PARAMETERS line are?

Code:
REST    35     1  OCTA

       2 !NTITLE followed by title
* COORDINATES OF PROT AFTER EQUIL
*  DATE:     2/12/ 9     16:50:24 

 !CRYSTAL PARAMETERS
 0.839232990331513D+02-0.167846598066303D+02 0.839232990331513D+02
-0.167846598066303D+02-0.167846598066303D+02 0.839232990331513D+02
 0.159429497600285D-02 0.000000000000000D+00 0.000000000000000D+00
 0.000000000000000D+00 0.000000000000000D+00 0.000000000000000D+00
-0.527290357144137D-01 0.205089171713813D-01-0.248807127981748D-03
 0.872657979334655D+02 0.872657979334655D+02 0.872657979334655D+02
 0.109471220634492D+03 0.109471220634492D+03 0.109471220634492D+03
 0.344937884361168D-01 0.344937884361168D-01 0.344937884361168D-01
 0.000000000000000D+00 0.000000000000000D+00 0.000000000000000D+00
 0.436328989667328D+05 0.436328989667328D+05 0.436328989667328D+05
 0.547356103172458D+05 0.547356103172458D+05 0.547356103172458D+05
 0.380766033939294D+07 0.380766033939294D+07 0.380766033939294D+07
 0.599197407360269D+07 0.599197407360269D+07 0.599197407360269D+07
 0.343735460532467D+03 0.171867730266233D+06 0.150704865600781D+03
 0.704330116716081D+08

 !NATOM,NPRIV,NSTEP,NSAVC,NSAVV,JHSTRT,NDEGF,SEED,NSAVL
       51801       65000       50000         500         500           0      105340 0.184847159300000D+10           0

 !ENERGIES and STATISTICS
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT


I suspect that the first two lines give the coordinates of some the unit cell vectors, but why two lines and which values are the X,Y and Z coordinate, resp? The 7th line should give the angles between the unit cell vectors for the truncated octahedron. I initially thought that every row corresponds to one of the 14 image transformations needed for OCTA, but it is obvious this should not be the case (since the 7th line is just angles).

I would appreciate any information that can help me find out the correspondence between the values and the variables behind them.

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rmv Online Content
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Have you checked the source code yet?


Rick Venable
computational chemist

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mittko Offline OP
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Yes, but not every single piece. I did not find the code that writes out the restart files, especially the CRYSTAL data section (c35b1/source/io/* /c35b1/source/image/*). I might have missed it, but suggestions on where to look for it would be helpful.

The inexplicable for me thing is why when a user needs to know something about the format of the files and what actually they consists of they apparently have to sink themselves into the messy code. There is no such information in the documentation (only brief discussion about the PDB/CRD formats).

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rmv Online Content
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The restart files were not intended to be read or manipulated directly by humans. Check the WRIDYN subroutine in

source/dynamc/dynio.src


Rick Venable
computational chemist


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