RE: Constant z axis

From: Navdeep (navdeep79_at_gmail.com)
Date: Sat Oct 11 2008 - 22:25:56 CDT

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               Fax: 217-244-6078

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