How to plot rmsd of amber trajectories in time unit ns using cpptraj ?

Hi,

you could try the "time" keyword in rms command.

I don't know how many frames there are in your trajectory, but assuming you are saving your coordinates after each 1 ps, you could try typing:

rms ToFirst :1-81&!@CA,C,N,O*= first out rmsd1.agr time 0.001 mass

Hope that helped.

Karolina

Barış Kurt

Sadaf Rani first I am sorry I know it has been too late but I really saw your question now.

Here is answer-1:

All information you need are in the *.out files. So you can use awk and grep and even paste commands in linux to merge times(ns) with energies.

Code example:

LEt's say after molecular dynamics you have md1.out md2.out md3.out exc.. files... and you need to write a file including time(ps or ns) and energies.

1. extract time(ps) from *.out file and write it as an ".a.txt" file:

grep "TIME(PS) =" *.out | awk '{print $5 " " $6 " " $7 " "}' > a.txt

2. extract energies (let's say potential energy) and write it as a "b.txt"

grep "EPtot" *.out | awk '{print $8 " " $9 " " $10 " "}' > b.txt

3.now merge a and b file from left to right:

paste -d ' ' a.txt b.txt > energies_with_time.txt

now your energies_with_time.txt file must be like this:

TIME(PS) = 31211.600 EPtot = -176097.5485

TIME(PS) = 31212.000 EPtot = -176054.5625

TIME(PS) = 31212.400 EPtot = -175818.6716

TIME(PS) = 31212.800 EPtot = -175828.6955

TIME(PS) = 31213.200 EPtot = -176179.1760

TIME(PS) = 31213.600 EPtot = -176142.4962

TIME(PS) = 31214.000 EPtot = -175929.3474

TIME(PS) = 31214.400 EPtot = -176099.3538

I tested these commands and saw that they worked. I used AMBERTools16 you may edit "$5-6-7" numbers according to your files.

answer-2:

in python: in this url apply instructions until the title of "Plot RMSD v Time" https://ctlee.github.io/BioChemCoRe-2018/rmsd-rmsf/

Yoshinobu Ishikawa

Hi Garima,

You can plot cpptraj.out by Excel, and multiply frame number by time interval.

Garima Singh

Thanks Yoshinobu and Karolina your suggestion is working for me.

I want to run my Amber MD calculation in HPC. How to perform MD calculation using AMBER 14 in HPC .Which script file i need?

Kindly provide your valuable suggestion

Thanks

Hi again,

You should check the following tutorials:

http://ambermd.org/tutorials/basic/tutorial1/section6.htm

http://ringo.ams.sunysb.edu/index.php/2017_AMBER_tutorial_with_4qmz

**you didn't state how many frames are there for every 1 ns??

trajin xxxx.crd 20 last 5

That means: get RMSD using Test1.crd from frame 20 to the last frame, skipping by 5 frames...

Sadaf Rani

Barış Kurt I have 2000 frames in my trajectory file and I am giving following command to cpptraj:- rms first :1-492@CA= first out rmsd424.agr mass time 1.0 but still I am getting graph in number of frames rather than time. How should I change it in to time in ns?

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