RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hello, I assume that you mean pull_pbcatom0... Nothing changes when I set this to an atom index I am afraid. I saw that you had use pull_geometry=cylinder in your recent JACS paper. Would it be too much to ask to see those pull settings? I simply cannot get the molecule to stay at the desired z-po

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

> Does the cylinder geometry work if you use "pull_start = no" and pull_init1 > equal to your starting (restraint) distance? I'm just trying to go through > all > of the iterations of what might be failing. In theory, what you're doing is > fine but I'd be interested to know if there was som

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

> 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? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull= umbrellapull_geometry

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hi, the distance is 3.89 nm and the z-dimension is roughly 8 nm > Date: Sat, 28 Apr 2012 09:18:31 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with > pull_geometry=cylinder > > > &

[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hi. I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer. In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder. Whenever I run a short simulation with umbrella sampling starting from a configuration with