Hello Ben,
I tested DPPE/DPPG with 15-20 surface tension and a cutoff of 10 angstroms.
Maybe I found the same problem that the tails are highly ordered. Is there
the same problem with DOPC/DOPE/DOPG?
Thank you very much.
2012/6/17 Benjamin D Madej <bmadej.ucsd.edu>
> 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 - 11:00:03 PDT
