Question regarding NAMD membrane tutorial

From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Jan 31 2011 - 10:49:07 CST

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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