Hi Garima,

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

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

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