[gmx-users] g_hbond

fahimeh baftizadeh fbaftizadeh at yahoo.com
Fri Sep 17 19:32:30 CEST 2010

Thanks for the reply.
In fact I had the trajectory with water but then I removed it to have smaller size of files. the point is that It didn't complain or crash when I was using that trajectory, choosing water in the groups selecting. but it didn't also generate any output. that is why I asked that ...

Anyway since I have gro files time to time, I think I will cat all the gro file and use that for analysis of h_bond.  

--- On Fri, 9/17/10, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] g_hbond
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Friday, September 17, 2010, 9:37 PM

On 9/17/10 5:37 PM, Justin A. Lemkul wrote:
> Fahimeh Baftizadeh Baghal wrote:
>> hello,
>> I have a trajectory generated by gromacs in which I excluded water and
>> there is only protein, now I like to see how does the number of h_bond
>> between water and protein change during the trajectory. In fact when I
>> use g_hbond I can choose the water and protein but I was wondering
>> where does the information about water come from??
> Certainly you can choose whatever groups are present (either from
> default groups or from those in an index file), but I would imagine the
> command will either fail or simply identify that there are no hydrogen
> bond donors or acceptors within what would otherwise be water.
> If you have not saved the coordinates for water, you cannot run any
> command to analyze properties related to or involving water.

In theory you could get an approximate number from analyzing what polar 
groups are not hydrogen bonded intramolecularly. There is not ready tool 
to do this. The quickest solution is probably to rerun the simulation. 
In most cases human time is more valuable than computer time.

> -Justin
>> thank you in advance for your time
>> Fahimeh

David van der Spoel, PhD, Professor of Biology
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
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