Hello Tales,
In our MD simulations with Lipid11, DOPC does much better than DPPC. Although the carbons with saturated bonds are still too ordered, the overall intrinsic disorder of the bilayer tails is maintained in the final DOPC structure.
The saturated acyl tails, in general in Lipid11, are too highly ordered.
Like I said in my previous email, increasing the cutoff did not significantly impact this issue.
We're currently refining new parameters to address this for the next release of the lipid force field.
Ben Madej
Walker Molecular Dynamics Lab
On Jun 16, 2012, at 10:49, "Tales Yuan" <yukitenkou.gmail.com> wrote:
> 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 - 11:30:02 PDT
