[gmx-users] Cylinder pulling through bilayer

[Gmx QA]

Anyone?

Thanks again
/PK

2017-06-07 21:22 GMT+02:00 Gmx QA <gmxquestions at gmail.com>:

> Dear list
>
> I am attempting to pull a small molecule though a bilayer using the pull
> geometry cylinder with gromacs v 2016.
>
> This is the relevant portion of my mdp-file:
>
> pull                      = yes
> pull-ngroups             = 2
> pull-ncoords             = 1
> pull-coord1-groups       = 1 2
> pull-group1-name         = LIG
> pull-group2-name         = MEM
> pull-coord1-type         = umbrella
> pull-coord1-geometry     = cylinder
> pull-coord1-rate         = 0.1
> pull-coord1-vec          = 0 0 1
> pull-coord1-k            = 1000
> pull-coord1-start        = yes
> pull-coord1-init         = 0
> pull-cylinder-r          = 1.5
>
> The pull-rate is very fast because I'm only doing preliminary test. At the
> start, the drug molecule is in -z position compared to the membrane.
>
> When doing grompp:
>
> $ gmx grompp -f umbrella_md_test.mdp -c npt.gro -p topol.top -o
> pull_test.tpr
>
> The output makes no sense:
> Using a fourier grid of 72x72x192, spacing 0.113 0.113 0.111
> Pull group  natoms  pbc atom  distance at start  reference at t=0
>        1        36        18
>        2     32500     64286        -nan nm           -nan nm
> Estimate for the relative computational load of the PME mesh part: 0.44
> This run will generate roughly 14 Mb of data
>
>
> I.e. nan's for distance. If I however switch in the mdp file so that
> pull-group1-name = MEM and pull-group2-name = LIG, the distance gets
> correctly calculated. But this does not seem to be what is prescribed in
> the manual for cylinder pulling, where is says that the cylinder is formed
> from the first group (should be the drug molecule) and through the com of
> the reference group (the membrane in my case),
>
> I think there is something I am missing?
>
> Thanks!
> /PK
>