How to concatenate the pullf.xvg files

User discussions
1

GROMACS version: 2019.4
GROMACS modification: Yes/No

Dear Gromacs users,
I have simulated the Umbrella Sampling with lipid bilayer system.
After I run simulation, I run ‘gmx wham’ and noticed that the system does not converge.
So because I wanted to run simulation in succession, I used the command line below:

gmx convert-tpr -s SAMPLING/dist_23/md_umbrella_23.tpr -o SAMPLING/dist_23/md_umbrella_23_next.tpr -extend 800000
gmx mdrun -deffnm SAMPLING/dist_23/md_umbrella_23_next -cpi md_umbrella_23.cpt -noappend

But in prompting the ‘gmx wham’ there is need to concatenate the previous pullf.xvg file and pullf_next.xvg file.

Is there any way to address the situation?

Thank you.

2

They’re just text files. You can combine them with whatever text editor you like (or Linux cat).

3

Thank you for your reply, jalemkul

As I know the pullf.xvg file has time values in first column and force values in second column, I concerned about whether ‘gmx wham’ is independent of time or not

Does not merely concatenating two files(pullf.xvg and pullf_next.xvg) raise any problem?

4

The time values should be sequential since you are continuing a run. The only thing you’ll have to remove are the intervening header/comment lines in pullf_next.xvg.

5

Ah Oh very very thank you! :) bb