Wrong numbers of atoms in groups obtained with make_ndx

User discussions
1

GROMACS version: 2022.5
GROMACS modification: PLUMED 2.8.3 patch

Dear GROMACS users and developers,
I would like to use make_ndx to create groups of atoms to be subsequently used with gmx angle. I am interested in dihedrals.

In my system I have 256 identical molecules and of course the atoms have unique names. So, every group for dihedral angles must contain 256*4 = 1024 atoms.

Some groups contain the correct number of atoms, while some other groups contains more or less atoms than expected.

I also tried to use mk_angndx but it gives an empty file.

Do you know which may be the issue and how I can solve it?
Moreover, has this issue an impact only on indeces or can it affect also the simulations themselves?

I thank you in advance for you suggestions.

Thanks and best regards,
Tommaso

2

Make sure that your topology file has angles and dihedrals defined when you want to make use of mk_angndx.
You can check your apr file by using gmx dump.

Arun

3

Hi,
thanks a lot for your reply and for your suggestion - I was not aware of this gmx dump utility, so good to know.

I tried to run gmx dump, using the following command:

gmx dump -s Dyn.tpr -param -nonr > Gmx_dump.dat

The bonded interactions are equal to the ones listed in the topology.
I ran again mk_angndx, and I discovered that I made a mistake - I am interested in dihedral angles, but I needed to specify “-type ryckaert-bellemans” instead of “-type dihedrals”.
In this case mk_angndx worked since I obtained a non-empty index file, here called angle.ndx.

But when I run gmx angle:

image
image692×803 13.1 KB

I still obtain an inconsistent number of atoms in the groups in the index file.
Are there some mistakes from my side?

Thanks and best regards,
Tommaso

4

Hi difficult to say what is the mistake you are making.
Can you paste the error along with the input you provided.

5

Thanks for your reply.

The problem is that I do not receive any error message.

I try to build the index file that contains atom groups for dihedrals to further use it with gmx angle, but the number of atoms is wrong.

This is the sequence of operations:

gmx mk_angndx -s Dyn10.tpr -type ryckaert-bellemans -o angle.ndx
gmx angle -type ryckaert-bellemans -n angle.ndx -f Dyn10_whole.xtc

You can see the output from gmx angle (in terms of groups) in the image in my previous post.

No errors, everything works smoothly. Some groups seem to be not correct, because the correct number of atoms for each group should be 256*4 = 1024 since I have 256 identical molecules (= same compound) in the system.

6

Grouping is done based on dihedral/angle parameters. So if you have its/top you can look at the dihedral section and count the number of dihedrals that has parameters A1=3.26