From: Axel Kohlmeyer (
Date: Wed Mar 13 2019 - 16:18:12 CDT

On Wed, Mar 13, 2019 at 4:57 PM Giacomo Fiorin <>

> 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.

doesn't pbctools have a -centersel or something option, that can be used
instead of centering on the origin (which does nothing to remove a COM


> Giacomo
> On Wed, Mar 13, 2019 at 4:02 PM Rabeta Yeasmin <>
> 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

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.