Angular velocity autocorrelation function calculation

User discussions
1

Dear all,
Is there any tool for calculating the angular velocity autocorrelation function?
Thank you and Best regards,
Quyen

2

Checkout the rotacf tool. Not exactly what you are looking for maybe.

3

Thanks,
Seem this is exactly what I am looking for
Best regards

4

Cool! We used that recently for proteins in a publication that may be of interest:
https://pubs.acs.org/doi/10.1021/acsomega.9b02835

5

Dear Prof,
I see you answered some questions regarding velacc also, so I hope you can help me with that.

In the document of gmx velacc said: " With option -mol the velocity autocorrelation function of molecules is calculated. In this case the index group should consist of molecule numbers instead of atom numbers."

If the molecule of interest is 3 water molecules in Gro file is like this:

3252SOL OW27730 11.031 3.346 5.500 -0.3375 -0.2899 -0.0438
3252SOL HW127731 11.002 3.388 5.419 0.6101 1.0373 0.2730
3252SOL HW227732 11.110 3.393 5.525 0.1732 -1.5966 0.9202
3253SOL OW27733 9.685 9.675 8.306 0.1659 0.2956 -0.5813
3253SOL HW127734 9.730 9.700 8.225 0.4667 0.8002 -0.2629
3253SOL HW227735 9.613 9.738 8.313 -0.6068 -0.5062 -1.0860
3254SOL OW27736 6.849 1.484 4.312 0.5441 0.3690 -0.2759
3254SOL HW127737 6.756 1.502 4.294 -0.0594 -0.6504 1.6207
3254SOL HW227738 6.849 1.434 4.393 2.8466 1.2753 0.3629

what should be in the index file for gmx velacc calculation?
my command is:
gmx velacc -nonormalize -m -mol -n index.ndx -s topol.tpr

Thank you,
Quyen

6

It says you need the index for the molecule. It you have only water than the numbers in the index file would be
[ mywaters ]
3252 3253 3254

However if you have a protein the residue numbering may mess this up (since these numbers in the gro file are residues, not proteins). In that case subtract the number of residues - 1.

7

Sorry Prof,
In my simulation, the residue is not continuous.
Could you please look at my gro file and give me advice about this?

If I calculate for only 1 water molecule:
[ mywaters ]
3252

Then, I got an error that: The index group does not consist of whole molecules
Best regards,

8

I already answered that in the previous message. You want to have the molecule number starting from 1, which is DNA, likely there are two DNA molecules, then some protein, and the fourth molecule is your first water. In this way you compute the offset.

Even better, test it on a box with water alone.

9

Thanks, prof

10

Hi, again prof,
I make a test system, 348 water molecules( residue number from 1-348) and
I executed velacc for the first water, so my index file is:
[water]
1

with command:
gmx velacc -s …/md.tpr -f …/md.trr -mol -m -normalize -n index.ndx
I still got the error that:The index group does not consist of whole molecules

If the index file contains the atom index for molecules 1:
[water]
1 2 3
Then it works.
Thanks for your time!