VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 13 2019 - 15:34:12 CDT

If you want to "fix" in a new simulation, a distanceZ restraint on the
center of mass of the bilayer should do the trick. Use NAMD 2.12 or later,
so that Colvars will use the center of mass computed by NAMD in parallel.

For post-simulation analysis, pick a reference lipid or transmembrane
protein as the reference and wrap around that. Once all is wrapped around
that molecule, you can safely subtract the COM of the membrane in VMD at
every frame using a typical Tcl loop.

Giacomo

On Wed, Mar 13, 2019 at 4:02 PM Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Dear VMD users,
>
> I have run a simulation of protein inside lipid bilayer. It looks like
> during the simulation the lipid bilayer has moved in the z-direction
> significantly. I want to fix the centre of mass of the lipid bilayer at the
> origin so that through the whole simulation trajectories it keeps at the
> same position. I am wondering how can I do that.
> I have used the following command to do that but it did not work,
> *pbc wrap -sel "segid MEMB" -center origin -compound residue -all*
>
> Can anyone please help me?
> Thanks.
>
> Rabeta Yeasmin
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin