[gmx-users] water insertion in hbond analysis

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 24 21:58:53 CET 2006

Lydia wrote:
>    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.

the total number of HB is fine, as are e.g. the correlation functions. 
The -ins option does not work.

> Sincerely
> Lydia
> ------------------------------------------------------------------------
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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