From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 26 2007 - 08:18:24 CST
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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