[gmx-users] g_hbond question ... solvent insertion

[David van der Spoel]

On Thu, 2003-03-13 at 01:03, Senthil Kandasamy wrote:
> Hi all, 
> 
> I do not fully understand the -ins (Solvent inserted) option of
> g_hbond.when used, it provides an xpm with hbonds:  1. present 2.
> inserted and 3. present and inserted.
> What exactly are we calculating here? The insert.dat file shows, at a
> given time, a solvent (OW), a donor (N or OH) with a distance and an
> angle, and an acceptor (O) with a distance and an angle. What do these
> various angles and distances represent? Is there any reference that I
> can look at?
> 
Check the manual. At one stage we were interested in water inserted into
e.g. alpha helix hydrogen bonds.


> Thanks.
> 
> Senthil
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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