VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Thu Mar 14 2019 - 12:04:50 CDT

Thanks all for your suggestions.

Hi Jerome,
I am trying to install qwrap. But during the compiling process, it is
showing the following error-
q

*wrap.cpp:1:17: fatal error: tcl.h: No such file or directory #include
<tcl.h> ^*
*compilation terminated.*

Hi Giacomo,
I have tried the following two commands, but it lookd like it did not
change the position of lipid mass center.

*pbc unwrap -sel lipid*
*pbc wrap -center com -centersel lipid -compound residue -all*

I am wondering if I am using thw right commands.
Thanks.

Rabeta Yeasmin

On Thu, Mar 14, 2019 at 9:47 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>