[gmx-users] Fixing the molecule in the centre of the micelle

Alexey Kaa akabedev at gmail.com
Wed Nov 21 19:29:25 CET 2018

Dear Gromacs users,

I am wondering if you could help with advice. In my simulation I have a
drug that is initially put into the centre of a micelle. It tends to drift
away towards the micelle-water interface. I would like to run an umbrella
sampling simulation in order to get a potential of mean force function from
the centre of the micelle (let's assume it is spherical) towards bulk. If I
run energy minimisation and the NPT-equillibration the drug molecule (or
the micelle) already drifts away to the energetically more favourable
position, but obviously these steps must take place as otherwise we have a
non-balanced system. I tried to let the molecule equilibrate first and then
pull it through the center towards the opposite side of the micelle, but
then it rather rotates the whole micelle (even if I apply comm-mode Angular
to the micelle-building type of molecule), than goes through the centre. I
am wondering if it is possible to fix the centers of mass of both - the
drug molecule and also the center of mass of the micelle through the
minimisation/equilibration steps before applying the pull-code, but so that
the micelle-constructing molecules would equilibrate inside it and also the
pressure of water would become uniform outside? Or am I restraining the
rotation of the micelle wrongly?

API = drug, DLiPC = phospholipids making a micelle.
; mode for center of mass motion removal
comm-mode                = Angular
; number of steps for center of mass motion removal
nstcomm                  = 1
comm-grps                = API DLiPC


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