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

[Mark Abraham]

Both of those should be done in a script before calling grompp! There is
not yet enough reason to bother with the complexity of modifying initial
coordinates inside mdrun.

Mark
On Nov 28, 2013 6:27 AM, "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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