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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