Time evolution of one replica with temperatures from REMD

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes/No
Hello everyone, I am trying to analyze REMD data. I have run REMD for 32 replicas for 100 ns. For the first replica, I have 10 log files as I extended the simulation. I have concatenated them using cat. Then using the demux.pl script I could generate replica_temp.xvg and replica_index.xvg. Then I ran the following command -
gmx trjcat -f *xtc -demux replica_index.xvg -o traj.xtc
I obtain 32 different trajectories. My question is how do I obtain the time evolution of the first replica with respect to different temperatures? I tried with the edr file, but it looks like the replica remains at the almost same temperature throughout the simulation. Any help regarding this issue is highly appreciated. Thanks in advance!

2

Hi @Sanchari,
Did you find any solution for this query, as I am also stuck at the same step? If you are able to figure out please guide me as well.

Thanks

3

Hi @Shilpa we can plot the time evolution of the temperature from the xvg file obtained. It will depict which temperatures the particular replica is visiting.

4

Hi @Sanchari,
I did the below commands:

cat /sim{0…95}/remd.log > REMD_tot.log
demux.pl REMD_tot.log
gmx trjcat -f sim{0…95}/remd.xtc -demux replica_index.xvg

But I am not sure how to plot the time evolution of the first replica with respect to different temperatures…Could you please guide me?

Thank you!