[gmx-users] water insertion in hbond analysis

[Lydia]

   First thank you for your help and information.  Can I clarify this
question: Are the water mediated  hbonds  still counted as one per hbonded
water in the number of hbond as a function of time?  For example  suppose I
want to see number of hbonds from protein sidechains to sidechains and
choose water for -ins, are the water mediated hbonds still counted in the
number of hbonds as a function of time though their atome index are not
listed in the file insert.dat or hbond.ndx?   I see these lines around line
1988 are not commented out:
-----------------------------------------------------------------------------------------------------------------------------------------------------------
                        if (ins_d && ins_a && ihb) {
                          /* add to hbond index if not already there */
                          add_hbond(hb,ins_d_k,ins_a_k,h,grI,ogrp,
                                    nframes,TRUE,bMerge,ihb);
-----------------------------------------------------------------------------------------------------------------------------------------------------------
    Is it possible they are still counted in the number of hbonds as
function of time  graph (hbnum.xvg)?  Or they are not counted in currently
untill the bug is cleared.  Thank you for your help and sorry for taking
your time.

Sincerely
Lydia
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