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

[Jheng Wei Li]

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> 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>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>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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