VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 13 2019 - 16:18:12 CDT

On Wed, Mar 13, 2019 at 4:57 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
drift)?

axel.

>
> 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
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.