[gmx-users] Help with gmx make_ndx

[Mark Abraham]

Hi,

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Quyen said:
> thanks for your replying,
> I think if I type 8|9 then my index.ndx should not appear [systems] group
(
> it too large for my system)

Yes, it should, because you asked it to make a subset of a file that had
the full system...

> And if I use index of LA and CL in index.ndx to get coordinate from xtc
file, I got message: Segmentation fault (core dumped)

Next time, please explain the whole context the first time, which would
have gotten you a useful answer sooner. Probably you only wrote a certain
set of groups to your xtc file, so now you need an index group constructed
*relative to that set of groups* rather than *relative to the whole
simulation*. First, use make_ndx to make an index file that matches how you
chose in your .mdp file to save groups to your xtc file. Then use that
index file with e.g. editconf to make a subset of the coordinate file you
originally used with grompp. Then you have something you can pass to
make_ndx -f so that you can form your subset of the subset to extract the
coordinates of those ions from the XTC (assuming you saved them in the
first place).

Mark

On Tue, Aug 23, 2016 at 6:30 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> What do you think is wrong about the contents of the index group that was
> made?
>
> Mark
>
> On Tue, Aug 23, 2016 at 6:26 PM Quyen V. Vu <vuqv.phys at gmail.com> wrote:
>
>> Dear gromacs user,
>> my system contain such groups:
>>
>>   0 System              : 943920 atoms
>>   1 DNA                 :  3198 atoms
>>   2 LA                  :    76 atoms
>>   3 CL                  :   130 atoms
>>   4 Water               : 940516 atoms
>>   5 SOL                 : 940516 atoms
>>   6 non-Water           :  3404 atoms
>>   7 Other               :    76 atoms
>>   8 LA                  :    76 atoms
>>   9 CL                  :   130 atoms
>>  10 Ion                 :   130 atoms
>>  11 LA                  :    76 atoms
>>  12 CL                  :   130 atoms
>>  13 Water_and_ions      : 940646 atoms
>>
>> Now, I want to get index of La and CL ions then I type:
>>        gmx make_ndx -f em.gro -o index.ndx
>> at the make_ndx prompt I type: "8|9"
>> then in my index.ndx I get group [LA_CL], also get [system] group ( too
>> much index)
>> How can I use correct make_ndx?
>> Thank you.
>> --
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>