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

Jochen Hub jhub at gwdg.de
Thu Dec 13 21:20:12 CET 2018


I would use

pull-geometry = distance

with pull-dim = Y Y Y

between the COMs of the micelle and the drug. You can use this already 
during the energy minimization.

I would not use comm-mode = angular, this is meant for other applications.


Am 21.11.18 um 19:29 schrieb Alexey Kaa:
> 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
> Thanks,
> Aleksei

Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189

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