Re: Aw: [gmx-users] Umbrella sampling - position restraints

Thanks Justin, Stephan. I am running both and will post my observations soon. -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-position-restraints-tp5010405p5010422.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mail

Aw: [gmx-users] Umbrella sampling - position restraints

it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart.  A comparison however, would probably

Aw: [gmx-users] Umbrella Sampling

  >will get the PMF profile for my >ligand binding or ligand and two ions binding?   It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? Gese

Re: Aw: [gmx-users] Umbrella sampling- force vs time plots

On 7/9/13 7:38 PM, rookie417 wrote: Thanks Justin and Stephan, One more question, while pulling from the interior of a multiple monomer micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for position restraints on the reference group to keep the system intact. I am assuming t

Re: Aw: [gmx-users] Umbrella sampling- force vs time plots

Thanks Justin and Stephan, One more question, while pulling from the interior of a multiple monomer micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for position restraints on the reference group to keep the system intact. I am assuming that I have to use different pull_k1 for

Aw: [gmx-users] Umbrella sampling- force vs time plots

  From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a la

Aw: [gmx-users] umbrella sampling for two polymer interaction

Dear Jiom,   Look at justines tutorial, there's example pull .mdp.   Stephan Watkins   Gesendet: Donnerstag, 30. Mai 2013 um 14:44 Uhr Von: "gromacs query" An: "Discussion list for GROMACS users" Betreff: [gmx-users] umbrella sampling for two polymer interaction Dear All, I want to do Um