[gmx-users] Position Restraint File for grompp

[Francis Coleman]

Hi Kevin,

Thanks for your reply.

The protocol for maintaining cylindrical pores makes sense, but I'm still uncertain what command I should be applying. Could you please supply the command to generate files for restraining lipid tails to the center of the vesicle i.e. is it something comparable to gmx genrestr?

Thanks.

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________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin Boyd <kevin.boyd at uconn.edu>
Sent: Tuesday, October 30, 2018 7:59 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Position Restraint File for grompp

Hi,

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.
https://github.com/MayLab-UConn/BUMPy

Kevin

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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