Cluster Analysis without a trajectory file

User discussions
1

GROMACS version: 2018.4
GROMACS modification: No
Here post your question
I conducted simulated annealing 30 times in a loop and it generated 30 structures. Is there a way to do cluster analysis on these final 30 structures instead of using a trajectory file as input for gmx cluster?

2

gmx accepts one of the follow as options to specify for input files:

-f [<.xtc/.trr/…>] (traj.xtc) (Optional)

Trajectory: xtc trr cpt gro g96 pdb tng

3

Just to add on to the previous answer, you can always make a trajectory file by feeding your .gro configurations to gmx trjcat: http://manual.gromacs.org/documentation/current/onlinehelp/gmx-trjcat.html

4

  1. Error on using gmx trjcat with a gro file as input:
    It can only handle binary trajectory formats (trr, xtc, tng)

  2. Question: Is there a way to use multiple gro files as input and convert them all into a single trr file? And then use that as input for gmx cluster?

5

Apologies, it looks like there was some misleading documentation for trjcat (see: https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg39054.html). You will have to convert each .gro to .xtc using trjconv and then concatentate.

6

While possible, this is unnecessary; since .gro and .pdb files are just text, use the standard Linux cat command to make the multi-frame “trajectory” file.

cat *.gro > traj.gro