Hi Arjun,

Is it not as simple as:

trjcat -f 1.gro 2.gro 3.gro ... 20.gro -cat -o output.trr

Faidon

Hi Arjun, 

trjcat command should help you, take a look at this http://manual.gromacs.org/programs/gmx-trjcat.html

If you have the numbers in order and no other .gro file in the same folder, you can do:

trjcat -f *.gro ...(all the flags that you want) -o trajectory.trr

My solution to this problem has been to specifically declare the time-steps in a simple text file.

For a lot of individual snapshots (.pdb or .gro)

`0 1

1 2

2 3

3 4

....`

For concatenating longer trajectories it would read out more like:

`1 10000

10001 20000

....`

You port this into trjcat with the flag: `-settimes < time.txt`

If you want to order a very long list of *.gro or *.pdb files you can place them on a single line in a file (list-pdbs-oneline.txt) and generate the timestep file (times-pdbs.txt) simultaneously:

Here is one I do when I have thousands of configurations to include:

#!/bin/bash

a=0; b=1;

for i in {1..10000}; do echo -n " trimer_${i}_${j}_${k}.pdb" >> list-pdbs-oneline.txt ; echo ${a} ${b} >> times-pdbs.txt ; let a=$((a+1)); b=$((b+1)); done

I can then run a trjcat:

trjcat -f `cat list-pdbs-oneline.txt` -o traj.xtc -settime < times-pdbs.txt

Works like a charm.

Dear Jacob

can you send me the files list-pdbs-oneline.txt and times-pdbs.txt. i want to try them with my data (225 snapshots pdb files). thx

For what the script that you provided?

Dear all

I am thinking to generate pdb snapshots from .xtc trajectory then add chain ID to them. Once added, i will merge them again into .xtc trajectory file.

However, i do not know how to add chain ID to all models of the pdb snapshots.

i tried to add chain ID to one pdb snapshot using gmx editconf but only one model was modified. Have you an idea about this? thx

Nabil Abid The list-pdbs-oneline.txt and times-pdbs.txt were generated from the commands I wrote in my answer above:

#To make list-pdbs-oneline.txt

for i in {1..10000}; do echo -n " files_${i}.pdb" >> list-pdbs-oneline.txt; done

#Could use .pdb or .gro. The point is to make a long, single line of all the files I want to use and port it through the trjcat "-f" flag.

#To make times-pdbs.txt

a=0; b=1

for i in {1..10000}; do echo ${a} ${b} >> times-pdbs.txt ; let a=$((a+1)); b=$((b+1)); done

#This is to make a list of timesteps for each of the 'pdbs' above, so they all get loaded in frame-by-frame.

I hope this helps.

thank you Jacob Miner. it works nice.

please if you can help me in adding Chain ID to all models of pdb snapshots.

I am not aware that gromacs can do that itself.

How many chains are we talking?

it is only one chain but the problem that i am using gRINN program for the analysis of residue network during MD simulation. It requires 3 files: .xtc, .tpr and .top files.

Each time i run the program i get the error as mentioned in the figure. The first star.pdb file in my MD has chain ID so i duno where is the problem.

Well the issue is you may not be able to reclassify the whole .xtc.

What is the gRINN program supposed to do exactly?