Potential of Mean force for non-equillibrium simulations

User discussions
1

Please help me on how to find PMF (Potential of Mean Force) for non-equillibrium SMD simulations using Jarzynski equality… I have drawn Force vs Distance curve using pull data of my simulations but now I am completely stuck on how to proceed for PMF…

2

Hi Akki,
use gmx wham to get PMF.

3

Hi Akki,
as srahul correctly pointed out: You can use the gmx wham method to calculate a PMF from your SMD simulations. A good starting point to get used to the method would be the tutorial by Justin Lemkul (Umbrella Sampling). If you need further help, you should provide a little bit more information what you have tried so far.

Cheers,
Marius

4

Thanks for the reply @srahul and @Marius… But actually I am not following umbrella sampling procedure… I am performing non-equillibrium SMD simulations, in which it is not possible to calculate PMF using gmx wham, we have to use Jarzynski equality (equation) to find relation between work done and Free energy…
But the problem is I am unable to figure out How to apply my SMD result in that equation?
Please help me with that…

5

Hi Akki,
I think you will get your answer from this discussion Re: [AMBER] How to calculate PMF using Jarzynski�s equality? from Adrian Roitberg on 2013-01-29 (Amber Archive Jan 2013)

thanks
Rahul

6

Thanks @srahul… I will check it…