[gmx-users] using groups in index for gmx select

Sahithya S Iyer sah2714 at gmail.com
Wed Jun 14 06:44:56 CEST 2017


Hi gmx users,

Can anyone please tell me how to use a group in index file in gmx select.
For example -

*gmx select -n index.ndx -select 'name "OH2" and within 2 of com of name "P
and r 1-36"' -on P-water.ndx -s step7_production.tpr*

does not write out anything in the index (P-water.ndx) file. I have defined
this group in the index file. Can I use this in the -select command? If so,
how ?

 Basically I would like to select oxygen atoms of water molecules that are
2 nm around the phosphate groups of one monolayer.

Any help is much appreciated.
Thanks in advance.


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