From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 14 2019 - 12:37:58 CDT

"apt install tcl-dev" will select the right one for you.

On Thu, 14 Mar 2019 at 18:33, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Hi Jerome,
>
> When I searched for tcl development files, I got several things in the
> following website-
> *https://packages.ubuntu.com/search?keywords=tcl-dev
> <https://packages.ubuntu.com/search?keywords=tcl-dev>*
> I am wondering if you can please let me know which one exactly I should
> use.
> Thanks.
>
> Rabeta Yeasmin
>
> On Thu, Mar 14, 2019 at 12:20 PM Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> You need to install the Tcl development files, which under Linux might be
>> in a package called tcl-devel or something similar.
>>
>> Jerome
>>
>> On Thu, 14 Mar 2019 at 18:05, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>> wrote:
>>
>>> 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
>>>>
>>>