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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