normal Why "HIS0", "W", "NA", "CL" are not recognised as indices for "gmx trjconv"?

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2 months 2 weeks ago #8037 by lanselibai
I use gromacs 2018.2 for my MD. After using the "gmx trjconv" command, the prompt is:

$ Group 0 ( System) has 72758 elements
$ Group 1 ( Protein) has 9140 elements
$ Group 2 ( Protein-H) has 9140 elements
$ Group 3 ( C-alpha) has 0 elements
$ Group 4 ( Backbone) has 0 elements
$ Group 5 ( MainChain) has 0 elements
$ Group 6 ( MainChain+Cb) has 0 elements
$ Group 7 ( MainChain+H) has 0 elements
$ Group 8 ( SideChain) has 9140 elements
$ Group 9 ( SideChain-H) has 9140 elements
$ Group 10 ( Prot-Masses) has 9140 elements
$ Group 11 ( non-Protein) has 63618 elements
$ Group 12 ( Other) has 61462 elements
$ Group 13 ( HIS0) has 240 elements
$ Group 14 ( GLU0) has 220 elements
$ Group 15 ( ASP0) has 40 elements
$ Group 16 ( W) has 60962 elements
$ Group 17 ( NA) has 948 elements
$ Group 18 ( CL) has 1208 elements
$ Group 19 ( Ion) has 2156 elements
$ Group 20 ( HIS0) has 240 elements
$ Group 21 ( GLU0) has 220 elements
$ Group 22 ( ASP0) has 40 elements
$ Group 23 ( W) has 60962 elements
$ Group 24 ( NA) has 948 elements
$ Group 25 ( CL) has 1208 elements

Can I ask

1) I can confirm that the "Protein" group does not include "HIS0", "GLU0" and "ASP0". Is there a way to include them by default?

2) why some groups are shown twice here (e.g. W, HIS0)?

3) I can use either "1" or "Protein" without any problems, but got problems for "HIS0", "W", "NA", "CL".

For example, if I type "HIS0", I got error:

$ Select a group: HIS0
$ Error: Multiple groups 'HIS0' selected
$ Error: No such group 'HIS0'

but if I type "13", I got no problem:

$ Select a group: 13
$ Selected 13: 'HIS0'

However, I can use "echo W | gmx genion" without any error. So why "gmx trjconv" got errors for typing "HIS0", "W", "NA", "CL"?

4) The Boolean Operators NOT, AND and OR could not work. For example

$ Select a group: System NOT Protein

got error:

$ Select a group: Error: No such group 'NOT'


5) So to work around, I have to mannually do the indices

Thank you!

Yours sincerely
Cheng

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2 months 2 weeks ago #8039 by peterkroon
Hi Cheng,

this is more of a Gromacs question, but ok.

4) You're using the wrong syntax. NOT == !, AND == &, and OR == |. `!13` would work.

3) genion != trjconv, especially when passing index files to one but not the other.

1) No, not that I'm aware of. Not without messing with the Gromacs code anyway.

2) Probably due to the exact commands used to arrive at this point. Some of those groups are created by default, and apparently some more than once.

5) The best way forward is to create your own index file with either `gmx make_ndx` or `gmx select`, and use that index file for the rest of the analysis/conversion. You'll get best results if you make it from a tpr file.

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2 months 2 weeks ago #8041 by lanselibai
Hi Peter,

Thank you for the help!

1) okay, the "Protein" group could not include "HIS0" by default.

2) okay.

3) Sure, the syntax in genion and trjconv are different.

4) Thank for correcting the Boolean Operators

5) Sure, I will do the "gmx make_ndx".

Cheng

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