Hello all,
To add my two cents: I did a simple test with Lipid11, surface tension, and the cutoff distance for DPPC. We have had trouble simulating DPPC because the saturated alkyl tails are still too highly ordered. We wanted to see if increasing the cutoff distance would have an effect on the bilayer structure, especially the alkyl order parameters.
The first simulation was with 128 DPPC phospholipids, 15 dyne/cm surface tension, and a cutoff of 8 angstroms. The second simulation was the same with a cutoff of 12 angstroms.
After 100ns, the results indicated that there was no significant change in the bilayer structural properties (area per lipid, electron density, order parameters). In particular, the DPPC saturated tails were still too highly ordered.
It seems like a some of the people in the field I have talked to insist on high cutoffs, but they don't have satisfactory explanations as to why.
The saturated acyl tail order is an issue we have been working on, and we are currently testing new parameters for their effect on the tail order and on the bilayer structural properties. We'd like to avoid the artificial constant surface tension all together with a parameter set that can run MD with the tensionless NPT ensemble.
Ben Madej
Walker Molecular Dynamics Lab
________________________________________
From: Albert [mailmd2011.gmail.com]
Sent: Saturday, June 16, 2012 10:01 the AM
To: AMBER Mailing List
Subject: Re: [AMBER] R: strange POPC under lipids 11 FF
On 06/16/2012 06:57 PM, Vlad Cojocaru wrote:
> Of course I understood that LIPID11 is a different story than GAFF. I just wanted to share my experience with GAFF and POPC. Indeed, we did not run long enough but with surface tension 45 we got below 62 after few ns.
HI Vlad:
What did you mean "we got below 62 after few ns". Did you mean your
lipids system becomes unstable?
best
Albert
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Received on Sat Jun 16 2012 - 11:00:02 PDT
