Hi all,
When attempting to run gmx bond, there is a message with a link to a defunct page. Is this functionality lost at this point? Granted, simple enough to script, but thought I’d ask first. Thanks!
Which link? Are you referring to h-bond?
No, the tool is still alive and in newer GROMACS versions you have two options, the new implementation (gmx hbond) and the old one (gmx hbond-legacy) which should be the same of older GROMACS standard gmx hbond.
As far as I can see, it (g_bond) hasn’t been around since version 4.6.7, so it hasn’t been available for more than 10 years. Is there any specific reason you need it? See if gmx distance can do what you want, based on Command-line reference — GROMACS 2016 documentation.
We should fix the message.
I have a structure with bonds defined in the topology, all as-is. All I need is the average of all bond lengths within that structure as a function of time, not things between what can be found in a normal index. I need code that will look at a bonds section inside an itp file and just go through the entire list for every trajectory frame to get the “ensemble” average for it.
Now, gmx distance will spit out the distances between indexed selections, which sounds like for what we want the index needs to be scripted in a silly way. Which also means we should just script what we actually need instead. Am I wrong?
Yes, you need pairs in the index file. You also needed that with g_bond. So, you could either script the index file generation or script the analysis. Perhaps MDAnalysis might be useful.
I honestly never used g_bond, but somehow assumed that it was the right choice for this simple task. Anyway, all well taken, thanks – we will whip something up.
Also, two weeks ago we almost named our new cluster Magnus. :)