[gmx-developers] How to utilize the index file in code? GROMACS 4.6.3

[Anton Feenstra]

My pleasure.

Let me just add that porting grompy to gromacs development version will 
be a bit of work, but possibly less than hacking mdrun on your own!
The grompy solution will be certainly more versatile and reusable.
Most importantly, I think, it will be much more reliable and less risky 
because you are not interfering with the inner md engine code.

https://github.com/GromPy/GromPy
http://onlinelibrary.wiley.com/doi/10.1002/jcc.22947/abstract

On 28/11/13 12:01, Jheng Wei Li wrote:
> Thanks for your advice and sharing, Anton.
> And thank /Mark too.
> /
>
>
> On Thu, Nov 28, 2013 at 5:58 PM, Jheng Wei Li <lijhengwei at gmail.com
> <mailto:lijhengwei at gmail.com>> wrote:
>
>     Hmmm, actually I modify it to do the Bsin Hopping,
>     so outside the mainloop I add a for_loop to do that and also change
>     the geometry...
>     That's why I need to trouble myself with that..
>     JhengWei Li
>
>
>
>     On Thu, Nov 28, 2013 at 1:26 PM, Jheng Wei Li <lijhengwei at gmail.com
>     <mailto:lijhengwei at gmail.com>> wrote:
>
>         Thank you to clarify my question, Anton.
>           In do_lbfgs that I am currently modifying,
>         the information I need to provide at first place is  about xx & ff.
>           My intention now is adjusting the coordinates before going
>         into the main loop,
>         like swap the xyz between two atoms which are different species,
>         or, later,
>         my adviser want to identify a molecule and rotate it before
>         doing the minimization.
>           Therefore, the first thought I jump out is reading the index
>         or atomtype, but it looks not trivial to me...
>
>         JhengWei Li
>         Institute of Atomic and Molecular Sciences,
>         Academia Sinica, Taipei 106, Taiwan
>
>
>
>
>         On Wed, Nov 27, 2013 at 11:33 AM, Jheng Wei Li
>         <lijhengwei at gmail.com <mailto:lijhengwei at gmail.com>> wrote:
>
>             Uhhh.. add something ...
>             After all, I just need to divide the system into some
>             subgroups,
>             I just want to call it and I don't need to change it!
>
>
>
>             On Wed, Nov 27, 2013 at 11:28 AM, Jheng Wei Li
>             <lijhengwei at gmail.com <mailto:lijhengwei at gmail.com>> wrote:
>
>                 Thank you, Mark.
>                 Or could I find a way to recall the atomtype?
>                 Will that be easier?
>
>
>                 JhengWei Li
>                 Institute of Atomic and Molecular Sciences,
>                 Academia Sinica, Taipei 106, Taiwan
>
>
>                 On Tue, Nov 26, 2013 at 9:44 PM, Jheng Wei Li
>                 <lijhengwei at gmail.com <mailto:lijhengwei at gmail.com>> wrote:
>
>                     Hello, all
>                        I am passing an index file chopping atoms into
>                     several subgroups, and
>                     I want to utilize this information in minimize.c!
>                     How do I recall index information in minimize.c?
>                     Please give me some advice or which part of code
>                     should I take a look to mimic its format!
>
>                     JhengWei Li
>                     Institute of Atomic and Molecular Sciences,
>                     Academia Sinica, Taipei 106, Taiwan
>
>
>
>
>
>


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
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|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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