GROMACS version:
GROMACS modification: No
Dear gromacs users, I am posting two questions regarding umbrella sampling. I hope to get answers.
So my first question is, do we need Pressure coupling while pulling during umbrella sampling?
And, should I position restraint the lipid bilayer during the pulling of a drug molecule through it? I think position restraining will not allow a natural passage for the drug.
Pressure coupling is is not coupled to umbrella sampling, so you choose pressure coupling, or not, the same way as for a system without pressure coupling.
Why would you want to position restrain the membrane? For pull a drug through a membrane you would usually use the pull code with cylinder geometry for the membrane. Then one should not use position restraints.
Thank you sir for the clarification.