Trjcat problem

User discussions
1

Hello! Nice to say hi, I am trying to join several paths, but when I apply the command

gmx trjcat -f run1.trr run2.trr run3.trr run4.trr run5.trr run6.trr -n indice.ndx -o parte1.trr -cat yes -overwrite yes -settime

It seems to me that it does not consider all the frames, since the 6 files are 3ps therefore I should obtain an ouput with 18 ps and I obtain one of 17ps.

I tried removing -settime, but it doesn’t work either. I saw in a previous thread that I could join two by two, but it still indicates a shorter simulation time.

Enter the new start time (ps) for each file.

There are two special options, both disable sorting:

c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
restarts with t=0.

l (last) - The time in this file will be changed the
same amount as in the previous. Use it when the time in the
new run continues from the end of the previous one,
since this takes possible overlap into account.

      File             Current start (ps)  New start (ps)

             run1.trr        0.000 ps          '' not recognized as a floating point number, 'c' or 'l'. Try again: c
             run2.trr        0.000 ps          c
             run3.trr        0.000 ps          c
             run4.trr        0.000 ps          c
             run5.trr        0.000 ps          c
             run6.trr        0.000 ps          c

Sorting disabled.

Summary of files and start times used:

      File                Start time       Time step

             run1.trr        0.000 ps        0.100 ps
             run2.trr        Continue from last file
             run3.trr        Continue from last file
             run4.trr        Continue from last file
             run5.trr        Continue from last file
             run6.trr        Continue from last file

Reading frame 0 time 0.000
lasttime 0

Continue writing frames from run1.trr t=0 ps, frame=0
Reading frame 20 time 2.000 → frame 20 time 2.000 ps
Reading frame 0 time 0.000
lasttime 2.9
Reading frame 1 time 0.100
Continue writing frames from run2.trr t=3 ps, frame=30
Reading frame 20 time 2.000 → frame 50 time 5.000 ps
Reading frame 0 time 0.000
lasttime 5.8
Reading frame 1 time 0.100
Continue writing frames from run3.trr t=5.9 ps, frame=59
Reading frame 20 time 2.000 → frame 80 time 8.000 ps
Reading frame 0 time 0.000
lasttime 8.7
Reading frame 1 time 0.100
Continue writing frames from run4.trr t=8.8 ps, frame=88
Reading frame 20 time 2.000 → frame 110 time 11.000 ps
Reading frame 0 time 0.000
lasttime 11.6
Reading frame 1 time 0.100
Continue writing frames from run5.trr t=11.7 ps, frame=117
Reading frame 20 time 2.000 → frame 140 time 14.000 ps
Reading frame 0 time 0.000
lasttime 14.5
Reading frame 1 time 0.100
Continue writing frames from run6.trr t=14.6 ps, frame=146
Reading frame 20 time 2.000 → frame 170 time 17.000 ps

Last frame written was 174, time 17.400000 ps

The amount of time is also less when I try to join only two files.

If someone has solved this problem please I appreciate their guidance

regards!

GROMACS version: 2018-1
GROMACS modification: Yes/No
Here post your question

2

Hi,
are those continuation runs? Did you try to run
gmx trjcat -f *.trr -n -o
Best regards
Alessandra

3

Hello Alevilla it worked, thank you very much for the guidance.

I’m new to gromacs and I have a bit of a hard time with syntapsis.

I have a simulation of two proteins and I would like to evaluate if they are in contacts and what residues they do.

For that I am applying

gmx mindist -f test1.trr -s md.tpr -n res.ndx -od od.xvg -tu ns

Y

gmx hbond -f test1.trr -s md.tpr -n index.ndx -contact -r2 0.5 -hbm test.xpm -hbn test.ndx

with the different ones for each command but I don’t understand how to tell me directly which are the interactions by residues as well as the hydrogen bonds.

If you can guide me I will be very grateful,

Greetings,

Paul

4

Hi,
It is better to open a new post for each issue/question. That will make the post more visible and accessible.

gmx mindist can provide the contacts between two groups and with the option -d one provide the distance that define a contact gmx mindist — GROMACS 2021.2 documentation

gmx hbond provides the hbond between two groups or within a group. gmx hbond — GROMACS 2021.2 documentation. With the option -a and -r you define the cutoff for the H-bond.
I never used the option -contact (gmx hbond) as you plan to use I think it was implement for the kinetic contact.

Best regards
Alessandra