From: Philip Blood (philb_at_hec.utah.edu)
Date: Fri Jan 26 2007 - 11:09:55 CST
The previous explanation by Morad is what I had in mind (didn't see that
before I posted).
Phil
Philip Blood wrote:
> Could you also use SMD and set the SMD velocity to 0 for either
> protein or lipids, and use regular constraints for the other one? I
> think this should work as long as you are OK with the center-of-mass
> of the atoms being constrained rather than each atom being constrained
> individually to a given location. I am actually trying this right now
> because I want to constrain the center-of-mass of a group of atoms,
> but only along a certain coordinate direction.
>
> Phil
>
>
> Peter Freddolino wrote:
>> Hi Himanshu,
>> I think your question was clear, but I hadn't had my coffee yet when I
>> answered ;-)
>>
>> You can't do both of these simultaneously with builtin constraints; you
>> would have to constrain the lipid using selectConstraints, and then use
>> a tclforces or tclbc script to constrain the protein (or vice versa).
>> Using selectConstraints will put ALL constraints only along the
>> specified coordinates.
>> Peter
>>
>> Himanshu Khandelia wrote:
>>
>>> Perhaps my question is not clear.
>>> I want to do the following in the same simulation:
>>>
>>> - Constrain lipids in the z-direction
>>> - Constrain the protein about its mean position
>>>
>>> Can this be done in the same script using the selectConstraints
>>> command ? Or will both the protein and lipids be constrained in the
>>> z-direction ?
>>> Thank you
>>>
>>> -Himanshu
>>>
>>> ----------------------------
>>> Himanshu Khandelia
>>> Research Assistant Professor (Postdoc)
>>> MEMPHYS, Center for Membrane Physics
>>> University of Southern Denmark (SDU)
>>> Odense M 5230, Denmark
>>> www.memphys.sdu.dk
>>> Phone: +4565503510
>>> email: hkhandel_at_memphys.sdu.dk
>>> -----------------------------
>>>
>>>
>>>
>>> On Fri, 26 Jan 2007, Peter Freddolino wrote:
>>>
>>>
>>>> Hi Himanshu,
>>>> you can have different values in the B column of all atom -- those
>>>> with
>>>> a 0.00 in that column will not be constrained.
>>>> Peter
>>>>
>>>> Himanshu Khandelia wrote:
>>>>
>>>>> Thanks Peter. SelectConstraints should work, except that I would
>>>>> want some of the atoms of the system constrained along the
>>>>> z-coordinate, and the rest of the atoms just to be constrained
>>>>> harmonically about their mean position.
>>>>> If I use a pdb file with the force constant values in the B
>>>>> column, would not all the atoms be constrained along the
>>>>> z-direction when using selectconstraints ? If so, is there another
>>>>> way out ?
>>>>> -Himanshu
>>>>>
>>>>>
>>>>>
>>>>> On Thu, 25 Jan 2007, Peter Freddolino wrote:
>>>>>
>>>>>
>>>>>> You may want to have a look at the selectConstraints feature
>>>>>> documented
>>>>>> at http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html, which
>>>>>> allow
>>>>>> you to constrain atoms only along certain axes.
>>>>>> Peter
>>>>>>
>>>>>> Himanshu Khandelia wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I am equilibrating a protein in a membrane. The simulation box
>>>>>>> initially has a larger area than the calculated area based on
>>>>>>> area per lipid, and the cross sectional area of the protein.
>>>>>>>
>>>>>>> In order to equilibrate it to the right area, I need to restrict
>>>>>>> the thickness of the bilayer, while allowing the area to reduce
>>>>>>> gradually under (preferably) NPT circumstances. Is there a
>>>>>>> harmonic potential in NAMD that can be enforce upon the
>>>>>>> headgroups to keep their average z-coordinate fixed ?
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> -Himanshu
>>>>>>>
>>>>>>> ----------------------------
>>>>>>> Himanshu Khandelia
>>>>>>> Research Assistant Professor (Postdoc)
>>>>>>> MEMPHYS, Center for Membrane Physics
>>>>>>> University of Southern Denmark (SDU)
>>>>>>> Odense M 5230, Denmark
>>>>>>> www.memphys.sdu.dk
>>>>>>> Phone: +4565503510
>>>>>>> email: hkhandel_at_memphys.sdu.dk
>>>>>>> -----------------------------
>>>>>>>
>>>>>>>
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