[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
chris.neale at mail.utoronto.ca
Wed Aug 15 20:55:59 CEST 2012
Write the authors of the simulation paper that has a "correct" APL for POPE and ask them for an input file.
That is really the only way to be sure that you are not doing something different than they did.
In my experience, people are quite willing to provide you with their input file(s).
If you still get a different APL than they reported, then see if your simulation times are similar and repeat your run
a few times to see if it's just statistical noise.
Regarding 323 K, I don't recall... it's just a number that sticks in my head. Perhaps it is for DPPE or DPPC.
I'd still suggest that you at least try POPC. So your peptide binds more favourably to POPE than to POPC...
that alone does not limit you to POPE. Then again, I don;t know exactly what you are trying to do.
-- original message --
My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE.
Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations?
At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list.
Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom.
I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?).
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