Re: Question regarding NAMD membrane tutorial

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jan 31 2011 - 11:11:43 CST

>From the userguide:
- useConstantArea <constant area and normal pressure conditions>
  Acceptable Values: yes or no
  Default Value: no
  Description: When enabled, NAMD keeps the dimension of the unit cell in
  the x-y plane constant while allowing fluctuations along the z axis.
  This is not currently implemented in Berendsen's method.

This permits fluctuation in the z-axis while keeping the membrane area
constant. This maintains the area-per-lipid while equilibrating the system.

Best,
Chris

--
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
snoze pa <snoze.pa_at_gmail.com> writes:
> Date: Mon, 31 Jan 2011 10:49:07 -0600
> From: snoze pa <snoze.pa_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Question regarding NAMD membrane tutorial
> 
> Dear NAMD Developer/Users,
> 
> I have a question related to two scripts used in NAMD membrane tutorials,
>  kcsa_popcwieq-03.conf  and kcsa_popcwieq-04.conf
> 
> If you calculate the difference between two scirpts then I observe that
> 
> 
> diff kcsa_popcwieq-03.conf kcsa_popcwieq-04.conf
> 
> 7c7
> < # Protein released. PME, Constant Pressure.
> ---
> > # Protein released. PME, Constant Pressure/Area.
> 15c15
> < outputName         kcsa_popcwieq-03
> ---
> > outputName         kcsa_popcwieq-04
> 21c21
> < set inputname      kcsa_popcwimineq-02
> ---
> > set inputname      kcsa_popcwieq-03
> 27c27
> < firsttimestep      502000
> ---
> > firsttimestep      752000
> 76,77c76,77
> < PMEGridSizeX       80
> < PMEGridSizeY       80
> ---
> > PMEGridSizeX       100
> > PMEGridSizeY       100
> 91c91
> < useConstantArea       no  ;# no for water box, yes for membrane
> ---
> > useConstantArea       yes  ;# no for water box, yes for membrane
> 123d122
> <
> 
> Both scripts are same.   Based on the tutorial I think kcsa_popcwieq-03.conf
> is  used to equilibrate the system while kcsa_popcwieq-04.conf is used to
> final MD run. If both scripts are same then how to justify that the script
> 03 is doing equilibration and 04 script is doing full MD run.  I will highly
> appreciate your help .
> 
> Thanks in advance for your time and help
> 
> S

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