Re: membrane constraints on thickness

From: Philip Blood (philb_at_hec.utah.edu)
Date: Fri Jan 26 2007 - 09:52:27 CST

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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