[gmx-users] Calculating the time for existence of h-bond

[Justin A. Lemkul]

minnu vijayan wrote:
> hello friends
> for doing normal mode analysis i am trying to create .mtx file .but in 
> output i am not getting thi .mtx file..what all precautions i have to take
>  
> with thanks
> 

To get the attention of someone who deals with normal modes, it would be best to 
start a new thread with an appropriate subject line.  Joining in on an existing 
thread with unrelated content will often get your question overlooked (or ignored).

Now, to attempt to answer your question.  There are many things that could be 
going wrong, but no one on this list can read your mind or figure out what 
exactly you're doing.  So here are some tips:

1. Post the text of your .mdp file
2. Show the *exact* command line you're using with mdrun
3. Provide the version of Gromacs you're using, at the very least, to rule out 
old versions and fixed bugs.  Information about your system and how Gromacs was 
compiled may be useful to ensure you did everything right.

Also consider how much memory your system might have in doing such a 
calculation, or writing such a matrix.  Also consider read/write permissions on 
the working directory.

-Justin

> 
>  
> On 11/20/08, *vivek sharma* <viveksharma.iitb at gmail.com 
> <mailto:viveksharma.iitb at gmail.com>> wrote:
> 
>     Hi All,
>     I am analyzing the h-bond information for a mdrun using g_hbond. Can
>     I know the % of  trajectory time for which a bond between particular
>     residue was existing?
> 
>     If anybody have tried such option please suggest me a way to do so.
> 
>     With thanks,
>     Vivek
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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