[gmx-developers] Free Format gro File
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 2 09:32:00 CEST 2012
On 2012-10-02 09:13, David van der Spoel wrote:
> On 2012-10-02 00:59, Jicun Li wrote:
>> You are right, Mark. Thank you very much for your suggestions.
> I think it is better to adopt another format altogether that is
> supported out of the box by other programs as well.
> SDF is such a format:
> It would be great to have native SDF support in gromacs.
OK, just to comment my earlier message: apparently SDF is also a fixed
format file, at least in the babel implementation (example below). It is
in Angstrom with 4 digits, and hence 100 times more resolution than gro
files (10 times more than pdb). The maximum coordinates are 99999
Angstrom or 9999 nm or < 10 micron. This is probably OK for a while for
atomistic simulations but not in the long run for coarse-grained models.
However, another drawback is that babel/the format only accepts elements
rather than atom names.
14 14 0 0 0 0 0 0 0 0999 V2000
-1.1900 -0.7290 0.2420 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1910 0.7270 -0.2420 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1140 -1.4190 -0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 2012/10/1 Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>>
>> On 2/10/2012 8:22 AM, Jicun Li wrote:
>> Maybe the fixed-format gro file is easier to code with in native
>> F77, but it's difficult to prepare with other molecule building
>> Sure, but once you've picked a file format, you're stuck with it for
>> a long time.
>> I would like Gromacs to read in the structure exactly, at least
>> as exact as g96 file. But I do not like to use g96 file because
>> there is no atom name in it. I can not use other software to
>> view the structure.
>> There's a separate library of code available on the website for
>> linking to external projects that want to write GROMACS-readable
>> trajectory file formats. That might be useful for you.
>> Wanting to write the atom names in the trajectory file is wasteful
>> if you have a big trajectory. For this reason, tools like GROMACS
>> and VMD can read a structure file and then import a trajectory file
>> that lacks atom information but whose atom ordering matches.
>> You'll be much better off using tools that suit the job at hand:
>> * When you want to view the structure, write a structure file
>> because it has atom names and stuff.
>> * When you want a high-precision trajectory, write a trajectory file
>> because it has high precision.
>> * When you want to view a trajectory, import the latter onto the
>> former. You may wish to reconsider your choice of viewer if you
>> can't do this :-)
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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