Clustering different chains and simulations

User discussions
1

GROMACS version: 2018.3
GROMACS modification: No

I have run 6 simulations of 100 ns with 4 peptides in each water box (all same peptide) and I want to do clustering with all together. I mean, generating clusters for the structures of the 6 simulations and of the 4 chains as if they belong to the same simulation. Do you know how to do that?

What I am able to do is to analyze each chain independently. For this, first I created an index with the independent chains:
gmx make_ndx -f md_0_1.gro -o chainA.ndx
4 & ri 1-12 #(Backbone for the rmsd)
1 & ri 1-12 #(Protein for the output)
And then I used that index to run the clustering:
gmx cluster -n chainA.ndx -f md_0_1.xtc -s md_0_1.tpr -method gromos -cl cluster.pdb -g cluster.log -cutoff 0.1 -b 50000 -dt 50 #(I only analyze the last 50 ns)

If I don’t select each chain, of course, I get clustering of groups of 4 chains.

So the problems for the clustering are two:
-How to compare structures from different simulations.
-How to compare structures of different chains in the same simulation.

For the first part I think in something like trjcat to combine simulations but for the second problem I have no clue.

Thanks.

2

Hi,
As far as I understood, you have 4 identical peptides in the simulation box and you want to cluster their structural feature (considering them as they were single molecule). From a technical point of view, you can save a traj file containing only 1 peptide each time (using gmx trjconv). Then analyze all the so-obtain trajectories togethers.
Note that the sampling of each peptide is affected by the presence of the other peptides.
Best regards
Alessandra

3

Hi,

Thank you. I have advanced a bit but still it is not solved.

I tried what you proposed. First I generated each independent trajectory:
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n 000cluster.ndx -b 50000 -dt 50 -o 0precluster11.xtc
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n 000cluster.ndx -b 50000 -dt 50 -o 0precluster12.xtc
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n 000cluster.ndx -b 50000 -dt 50 -o 0precluster13.xtc
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n 000cluster.ndx -b 50000 -dt 50 -o 0precluster14.xtc
(selecting Protein + each chain)

Then I joined the 4 trajectories in a new one:
gmx trjcat -f 0precluster1*.xtc -settime -o 0trajall1.xtc

And then I run the clustering:
gmx cluster -f 0trajall1.trr -s md_0_1.tpr -method gromos -cl cluster.pdb -g cluster.log -cutoff 0.1

But the file md_0_1.tpr seems not to be accepted. It does not fit with the trajectory file and it is a needed file.

Any solution for this?

Thanks.

4

Hi,
you can try to use an gro file containing only one peptide in box (e.i first snapshot of the trajectory) in place of the tpr or use the option -n index.ndx where you have one group with one peptide.

I notice that you generate first 0trajall1.xtc and than you use 0trajall1.trr as input in gmx cluster (I guess it is a typo).

Alessandra

5

Hi,

yes, it was a typo. I modified a gro file to have only one peptide and it works now.

Thanks a lot.