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

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

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 something

[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

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 On 4/28/12 5:12 AM, J B wrote