[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
john.b.86 at hotmail.com
Sun Apr 29 10:46:31 CEST 2012
> Is the problem specific to cylinder geometry? Do other settings work? Does it
> make a difference if you set values for pull_r0 and pull_r1?
I would think that it is the cylinder geometry that creates the problem.
If I use
pull = umbrellapull_geometry = distancepull_dim = N N Ypull_start = yespull_init1 = 0.0pull_ngroups = 1pull_group0 = DPPCpull_group1 = drugpull_rate1 = 0.0
The molecules stays in place. But pull_geometry=distance is what I would prefer due to the undulations.
Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the membrane...
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