How to pull a surfactant for umbrella sampling?

User discussions
1

Dear GROMACS user.

I am simulating a system consisting of Decane/water/surfactant. I would like to pull one surfactant molecule toward the water phase while the other surfactants remain intact, to calculate delta G using umbrella sampling (As I depicted in the attached image). I read the GROMACS tutorial for umbrella sampling. However, I don’t know how to pull just one surfactant. In the tutorial, the whole system was pulled while one part was constrained. How can I do that?
Also, Can I apply force on just one atom on the head of surfactant, for example?
Thanks

Picture1
Picture1991×449 17.8 KB

2

You can apply the pulling force to any subset of atoms in the system, so all you have to do to pull on one surfactant molecule is define it in an index group.

3

Dear Lemkul,

Thanks for your response.
How can I define to pull the surfactant to right or left? For example, to Z or -Z. is there any option in umbrella.mdp file?
Thanks again.

4 
pull-coord1-vec = 0 0 -1

vs.

pull-coord1-vec = 0 0 1