Re: Constant z axis

From: Nd S (navdeep79_at_gmail.com)
Date: Mon Oct 13 2008 - 12:27:23 CDT

Hello Chris

I am trying to run a simulation with carbon nanotube surrounded by some
matrix molecules (I am starting with water) inside a unit cell. The nanotube
is aligned along the z-axis and its length is equal to the initial z-axis.
After running NPT simulation, I want to keep this z-axis constant and only
want to have x & y axis changed.

Thanks
Navdeep

On Sat, Oct 11, 2008 at 10:59 PM, Chris Harrison <charris5_at_gmail.com> wrote:

> Navdeep,
>
> This isn't presently possible in NAMD. You can set x and y to a constant
> area and allow fluctuations in z, but the inverse isn't possible in the
> current code. Can you explain why you would want to do this? What type of
> simulation would benefit from an ability to freeze cell fluctuations in z
> but not those of x & y?
>
> Chris
>
>
>
>
> On Sat, Oct 11, 2008 at 10:25 PM, Navdeep <navdeep79_at_gmail.com> wrote:
>
>> Hi Chris
>>
>>
>>
>> Actually my question was: I want to keep the z-axis of the Unit Cell
>> constant and let only xand y axis to vary while running a NPT simulation.
>> How can I do that.
>>
>>
>>
>> Thanks a lot,
>>
>> Navdeep
>>
>>
>>
>> *From:* Chris Harrison [mailto:charris5_at_gmail.com]
>> *Sent:* Saturday, October 11, 2008 5:14 PM
>> *To:* Nd S
>> *Cc:* NAMD list
>> *Subject:* Re: namd-l: Constant z axis
>>
>>
>>
>> Navdeep,
>>
>> To keep z-axis coords of atoms fixed:
>> Option 1: Look at section 6.1.1 of the manual. Specifically,
>> "selectConstrZ".
>>
>> Option 2: Look at Tclforces in the manual (and then the online tutorial at
>> http://www.ks.uiuc.edu). You can create a restraint (with large force
>> constant) to hold atoms frozen (effectively).
>>
>> Chris
>>
>>
>> On Wed, Oct 8, 2008 at 7:59 PM, Nd S <navdeep79_at_gmail.com> wrote:
>>
>> Hi all
>>
>> I am doing NPT simulation.
>>
>> My questions are:
>> 1. I want to keep the z-axis constant, how I can do that.
>> 2. Do I have to use "useGroupPressure" if some atoms in the box are fixed,
>> or I can use the default settings.
>>
>> Thanks a lot,
>> Navdeep
>>
>>
>>
>>
>> --
>> Chris Harrison, Ph.D.
>> Theoretical and Computational Biophysics Group
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>
>> char_at_ks.uiuc.edu Voice: 217-244-1733
>> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
>> Fax: 217-244-6078
>>
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>

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