[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Bala S think_beyond at aol.com
Fri Apr 27 14:38:09 CEST 2012

Thanks Justin and Anirban for taking this long in TM simulations.

I'm following Justin's tutorial majorly and taking some clues from Anirban's
too when I need further clarification.

>From both of your guidelines I could understand wht I should be doing before
solvating the system. Now, I have a question that how many iterations I
should perform with inflateGRO program and what is the basis to stop and
move with solvation step?

Justin's one says that he could reach ~72 Å2 (which is above the expt. value
~62Å2). But when I am exactly following the tutorial with same KALP peptide.
I am ending up with 'Area per lipid: 3.73355898918962 nm^2' within 10
iterations which is far lower than Justin's. Why?


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