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

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 27 14:40:02 CEST 2012

On 4/27/12 8:38 AM, Bala S wrote:
> 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?

3.73 nm^2 is 373 A^2 - mind the fact that the units have a square term.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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