[gmx-users] Advice on High Precision Structure File Formats

David van der Spoel spoel at xray.bmc.uu.se
Sun Mar 4 19:09:18 CET 2012

Tot Ziens!

Op 4 mar 2012 om 18:44 heeft "Andrew DeYoung" <adeyoung at andrew.cmu.edu> het volgende geschreven:

> Hi,
> If you have time, I would be grateful for any advice you have about which
> structure file format that I should use.  I am attempting to create a carbon
> nanotube.  However, the carbon-carbon bond length that I would like to use
> is 0.1415 nm, which means that I would like a structure file format that can
> take positions up to accuracies of at least 0.0001 nm.  
> Unfortunately, the .gro file format only accepts positions up to accuracies
> of 0.001 nm.  This means that if I use .gro, I will need to round the
> carbon-carbon bond length to 0.142 nm or 0.141 nm, which I would prefer not
> to do.  
> Now, I know that the Gromacs code itself uses many more decimal places
> internally for running MD (single precision give a lot of decimal places and
> double precision gives even more).  I think this means that if I specify the
> carbon-carbon bond length in my topology as 0.1415 nm in [ bonds ] (and the
> .itp file format, and others, allow this type of precision) then even if I
> must use 0.142 nm in my starting configuration .gro file, the bond lengths
> will equilibrate to ~0.1415 nm if I run a short simulation (given that the
> Gromacs code internally uses high precision).
> Yet, what if I need my starting configuration to have high precision bond
> lengths (0.1415 nm)?  I plan to freeze the carbon atoms using a freeze
> group, and it would be easiest if I could do this from the get-go (i.e.,
> without running equilibration in which the carbon atoms are unfrozen).
> Do you have any advice about which file format I should use?  I need not be
> "constrained" by .gro
> (http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_ne
> ed_for_a_.gro_file).

> .pdb, it seems
> (http://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)#Example),
> gives position precision up to 0.001 ANGSTROM (or 0.0001 nm), which means
> .pdb will give me just enough precision.  Or should I instead write my
> starting configuration in a .g96 file, which allows very high position
> precision?  However, other than
> http://manual.gromacs.org/current/online/g96.html, I am having some
> difficulty (even with Google) locating detailed information about the .g96
> file format.  Unfortunately, my institution I do not think has a GROMOS-96
> license, so I cannot access its manual.
> Between .pdb and .g96, which would you recommend?  Or is there any other
> structure file format that I am not thinking of?
> Thanks so much.
> Andrew DeYoung
> Carnegie Mellon University
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