VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 14 2019 - 09:46:31 CDT

Yes, absolutely, "pbc -center com -centersel lipid" or "qwrap center lipid"
will both work, on either one of the two steps I suggested.

I prefer a two-stage approach because the computation of the center-of-mass
for the center selection assumes unwrapped coordinates, which may not be
available in the trajectory being read. One can first unwrap everything
(see Jérôme's suggestion), but this is much more time-consuming than
wrapping, even with qunwrap. If there is a protein (more precisely, a
protein subunit/fragment), this can be used as the center for the first
stage:

qwrap sel all center protein compound fragment
qwrap sel all center lipid compound fragment

Giacomo

On Thu, Mar 14, 2019 at 8:52 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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.
>>
> 

-- 
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