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.
-- 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:35 CST