[gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

[mahender singh]

Thanks for the advice

I will do this exercise with other molecule and will let you know the results.
but, why i was confused is because in one PMF curve all the free energy values are on the positive side where as the other has all free energy values on the negative side. do these signs are not important or there is something else. As What I understand is that if the free energy of the drug increases when going to the center of the bilayer, this drug cannot passively diffuse across the membrane (thermodynamically unfavored ).
I will try to go through more literature on this topic to understand this concept in more detail.

thanks you


with regards
Mahender Singh