VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 14 2019 - 12:20:05 CDT

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
>>
>