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

[Jheng Wei Li]

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> 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>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>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
>>>
>>
>>
>
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