Re: [gmx-users] Pulling inside a channel to calculate the PMF

Thanks Alex, finding the positions as you propose seems a legitimate way for this problem. One will have to wait enough with a classical MD but Bias MD should help. In my case the channel is not a large ion channel. FR. 2017-06-22 18:26 GMT+02:00 Alex : > I've never used

Re: [gmx-users] Pulling inside a channel to calculate the PMF

I've never used PLUMED, to be honest, so I don't know. If ligands are salt ions or any other overall charged entities, I would solvate the channel (with restraint, maybe) for essentially a production run and apply an electric field "parallel" to the channel lumen, then just visualize the

Re: [gmx-users] Pulling inside a channel to calculate the PMF

Hi Alex, There is no confusion about the pulling that is only a preparation for WHAM, but as you tell it you need to choose positions. These positions could be choosen manually: if one choose to explore the static channel from apo, then I'm agree, select the positions in the channel "in a bunch

Re: [gmx-users] Pulling inside a channel to calculate the PMF

I think your problem is solvable with enough perseverance, but there may also be some confusion... The PMF calculation isn't based on the data obtained from an actual pull: the pulling rate in those simulations is set to zero. The reason for using pull code there is to pull (pun intended) the