Re: Question regarding NAMD membrane tutorial

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Feb 03 2011 - 18:32:04 CST

No, there is a restraint. The periodic cell cannot change it's size in
the xy plane; however it can fluctuate in the z-axis. This means that a
membrane in the xy plane will not be able to easily spread out or
shrink (it is effectively restrained) and will therefore maintain
the area-per-lipid ratio for the membrane while utilizing the freedom
of the z-axis fluctuations to help allow the atoms of the membrane,
protein, water, etc to relax into an equilibrium state.

Is this clear for you?

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: Wed, 2 Feb 2011 13:03:38 -0600
> From: snoze pa <snoze.pa_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Question regarding NAMD membrane tutorial
> 
> Hi Chris and Valuable NAMD users,
> 
>  Thanks a lot for your reply. Somehow, my doubts are clear but if you check
> the script kcsa_popcwieq-03.conf carefully, which is used to equilibrate the
> system, there is no restrain at all. There is no pdb file coordinates that
> were used to retrain the protein. So Do you think it is like free dynamics.
> In all scripts there is a file name "fixedAtomsFile      nottails.fix.pdb"
> but it was never created in  NAMD membrane tutorials and examples.
> 
> Thanks
> S
> 
> 
> 
> On Mon, Jan 31, 2011 at 11:11 AM, Chris Harrison <charris5_at_gmail.com> wrote:
> 
> > 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 <http://www.ks.uiuc.edu/%7Echar>
> >  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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