[gmx-users] calculate *all* carbon atom distances over time?

Justin Lemkul jalemkul at vt.edu
Tue Feb 16 14:31:45 CET 2016

On 2/16/16 4:58 AM, Athina Meletiou wrote:
> Hi Justin,
> Sorry to be a pain (and for probably asking a silly question...) but could
> you maybe elaborate on how the shell script you mentioned yesterday would
> loop over all combinations of interest? I'm not asking you to tell me how to
> write the script - just a bit how the idea would work, as I'm stuck at the
> moment and don't get it exactly? So after I have my carbon atoms in
> individual groups in the index file, I would write a script that would
> combine the groups and invoke Gromacs' g_dist with that same script?


for ((i=0; i < 10; i++ ))
     for ((j=$((i+1)); j<10 && $j != $i; j++))
         echo $i $j | g_dist ...


> Also, another question, how can I quote the previous answer in my question?
> It would make it so much easier for you and for other readers to follow the
> discussion if I directly quoted your previous answer but I have no idea how
> to do it.

Just reply to the email like you would any other.  The message is sent to 
gmx-users and is then delivered to all the members of the list.


> Mark, thanks for the suggestion - I'll try that today. The funny thing was
> that someone with sudo rights did try to update cmake but after updating it
> we get the message that version 2.8.7 is the latest version. So I'll try a
> local install today and see.
> Thank you all, Athina
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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