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

[Alex]

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_to_calculate_the_PMF#594b792648954cf7f2759a48
> [accessed Jun 22, 2017].