[gmx-users] Essential Dynamics and Umbrella Sampling

[ANDRES ADOLFO ORTEGA GUERRERO]

Dear gromacs users,

I was wondering if you could help me with something, I did a simulation of
the permeation of a drug across an ion channel,
now due to the drug molecule is large and does not have symmetry i would
like to calculate the effect of the conformations of the
the drug and compare them with the pmf of the permeation.

I was thinking to do some Essential Dynamics Analysis, on each umbrella
sampling windows, but i dont know how this can be compared with the pmf? or
Do you think my idea is wrong?

Do you have any suggestion?,

I would really appreaciate your advices.
Thank you in advance for the time and help


Andres Ortega
Universidad del Valle, Cali-Colombia
Bionanoelectronics Research Group