[gmx-users] Position Restraint File for grompp

Kevin Boyd kevin.boyd at uconn.edu
Tue Oct 30 15:59:29 CET 2018


Depends on what kind of restraint you are trying to apply. If you're just
trying to restrain head groups during the initial equilibration period, you
can feed -r your actual structure, since the restraints should be relative
to current positions.

If instead you're following the pore-forming protocol used to equilibrate
between leaflets, then the tail coordinates are  just set to the center of
the vesicle. They're used for cylindrical flat-bottom potentials in this
case, which project out along the x, y, and z axis and repel the tails from
those cylinders.

Shameless plug for a tool developed in our lab that takes a more
quantitative approach to estimating interleaflet area distances so that you
can avoid a length pore-based equilibration.


On Tue, Oct 30, 2018 at 5:40 AM, Francis Coleman <jfd1g at outlook.com> wrote:

> Hi,
> I've been using CHARMM-GUI in an attempt to form coarse-grain vesicles but
> things aren't working out for one system. Before I start changing anything,
> I was wondering how the position restraint file for the lipid tails i.e.
> lipidtail_posres.pdb was generated. Or more generally, what is the command
> to generate a position restraint file that can be read by grompp with the
> '-r' option? In the past, I've only applied restraints to proteins and it
> was clear what  commands I required.
> Thanks.
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