[gmx-users] Docked ligand, umbrella sampling and "aiming"

[Jernej Zidar]

Edit:
  I tried to use the pull-geometry=direction and pull-vec but the latter
option doesn't work:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#

WARNING 1 [file md-pull-tune.mdp, line 69]:

  Unknown left-hand 'pull-vec' in parameter file
- - -

  The relevant part of the md-pull-tune.mdp is:

pull            = umbrella
pull-geometry   = direction
pull-vec = 1 0.5 0
pull-start      = yes       ; define initial COM distance > 0
pull-ngroups    = 2 ; number of groups involved in the pull
pull-ncoords    = 1 ; number of reaction coordinates
pull-coord1-groups = 1 2
pull-group1-name = Protein
pull-group2-name = BPA
pull-coord1-rate      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k         = 1000      ; kJ mol^-1 nm^-2

  The relevant section of the manual just mentions the "pull-vec"
option withou elaborating much on it:
http://manual.gromacs.org/online/mdp_opt.html#pull

  I use Gromacs 5.0.4.

Thanks again,
Jernej

On Fri, Mar 6, 2015 at 3:04 PM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> Hi there,
>   I have a receptor with a docked ligand. I would like to perform an
> umbrella sampling simulation to get some insights into the
> thermodynamics of the binding.
>
>   Following the Umbrella Sampling tutorial I performed the 500 ps
> pulling simulation. A visual examination of the trajectory revealed
> there's an expected change in the position of the ligand that is
> coincidental with a worryingly big increase in the force exerted on
> the ligand. Link to a figure:
> https://www.dropbox.com/s/fj3daaagimuynni/rec-lig-pos-for.pdf?dl=0
>
>   Is this an expected behaviour or should I try to somehow adjust the
> direction of the pulling? If so, could you advise on a strategy to do
> so?
>
> Thanks in advance,
> JZidar