VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 14 2019 - 07:52:07 CDT

Yup. Or if you want it to be quick, using qwrap (
https://github.com/jhenin/qwrap):

qunwrap sel lipid
qwrap sel lipid center lipid

Jerome

On Wed, 13 Mar 2019 at 22:57, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> 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.
>