How to plot pulling work and binding free energy after SMD?

User discussions
1

Hi everyone,
I have just got the SMD done. And now I’m on my way analyzing Pulling Work (W) and binding free energy (delta G). The Gromacs Tutorials doesn’t show to do it. I gave it a try searching on Google how to get these 2 things done. But I still cannot find out any infomation of how to do it.

Could you all possibly let me know how, or do you have any documents teaching about this?
Thank you for your help.

2

If you want to get work or binding free energy information from non-equilibrium simulations, you need to look at the classic Jarzynski paper on this and do many (many, many) SMD simulations. My tutorial does not address this because only one SMD run was performed, to generate windows for umbrella sampling.

3

Thank you sir very very much