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 <nedoma...@gmail.com>: > 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 trajectory and pick the configurations by hand. gmx trjconv > can -dump any particular frame of your liking. Maybe not as automated as > one could hope, but then you will know in-depth what configs you have. > > Alex > > > On 6/22/2017 3:03 AM, François-Régis Chalaoux wrote: > >> 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 of >> reasonably spaced spots along the curved "axis" of your channel, each >> followed by equilibration and the production run, yielding the data useful >> for WHAM". As you say, you need time and patience. Could PLUMED (or >> somethoing else) /Gromacs be used to automate this ? >> >> On the other side, this channel come from a static APO structure and the >> reality of this channel is tiedous, so why not discover dynamically the >> channel and run the next equilibration and the production run on the fly, >> could >> PLUMED (or somethoing else)/Gromacs be used to automate this ? How to >> discover the channel on the fly ? May be it is feasible to use simply the >> coordinates of the channel discovered by MDPocket with a long classical MD >> realized previously on the apo/holo structure ? >> >> FR. >> >> 2017-06-22 10:19 GMT+02:00 Alex <nedoma...@gmail.com>: >> >> 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 >>> positions and/or forces. The initial structures, of course, is where e.g. >>> Justin's tutorial uses pull along a straight line. >>> >>> However, if you have the time and patience, you could of course >>> (manually?) put your ligand in a bunch of reasonably spaced spots along >>> the >>> curved "axis" of your channel, each followed by equilibration and the >>> production run, yielding the data useful for WHAM. >>> >>> Hope this helps. >>> >>> Alex >>> >>> >>> On 6/22/2017 2:05 AM, François-Régis Chalaoux wrote: >>> >>> Hi everybody, >>>> >>>> I would like to pull a ligand in a channel from my protein and calculate >>>> the PMF with Umbrella sampling. This channel is probably not linear and >>>> thus have to be defined. Too much colisions appears along a simple one >>>> axis >>>> pulling and causing a catastrophic PMF calculation. >>>> >>>> Currently I'm working with Gromacs and I wondered if it is possible to >>>> define statically or dynamically the coordinates for the center of the >>>> channel and use it during the simulation (Pulling). >>>> >>>> One solution could be to define in the md_pull.mdp configuration file >>>> all >>>> the transition points of my pathway through which my ligand must pass >>>> from >>>> my APO structure determined with CAVER. >>>> Instantiation of Gromacs parameters of md_pull.mdp is not enough clear >>>> for >>>> me and PLUMED is may be a more direct solution. Currently I have no >>>> experience with PLUMED but It seems on paper to be able. >>>> >>>> An other choice would be to define dynamically the channel center, >>>> on-the-fly. PLUMED seems also capable to manage this sort of challenge >>>> but >>>> once again I have no idea of the feasibility of a such work. >>>> >>>> >>>> What do you think about this problem and of the tracks evoked above ? >>>> >>>> >>>> Cheers, FR. >>>> >>>> *Pulling inside a channel to calculate the PMF*. Available from: >>>> https://www.researchgate.net/post/Pulling_inside_a_channel_t >>>> o_calculate_the_PMF#594b792648954cf7f2759a48 >>>> [accessed Jun 22, 2017]. >>>> >>>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? 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