[gmx-users] Re: Measuring hydrogen bonding in a specific region

[Alex Marshall]

Thanks Justin, this is great.

On Tue, Jul 17, 2012 at 5:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/17/12 4:57 PM, Andrew DeYoung wrote:
>>
>> Hi Justin,
>>
>> I am just curious, do you have experience writing such a shell script to
>> iterate over the index files (one per frame)?  I am just curious, because
>> I
>> have been trying this, and I have found it very difficult to do using
>> bash.
>> Do you use a different shell language?
>>
>> Also, I wonder if anyone has ever posted such a shell script on this list.
>> When I look through the archives, I don't see one, but I could be wrong.
>>
>
> Assume we have 100 groups of arbitrary size and a fixed group (index group
> 0) in the index file to which we wish to calculate hydrogen bonds.  Then
> assume we have 100 separate files (from trjconv -sep or whatever else)
> numbered sequentially, i.e. conf1.gro, conf2.gro...conf100.gro.  A simple
> bash script that runs through the index groups corresponding to each of
> these coordinate files would be something like:
>
> #!/bin/bash
>
> for i in {1..100}
> do
>     echo 0 $i | g_hbond -s topol.tpr -f conf$i.gro -n index.ndx
> done
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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-- 
Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario