Dear Adrian,
here I agree with Vald completly.
Colleagues from Prague, showed, that in long simulations, the charmm ff
parameters are also not appropriate, only with surface tension (Siu &
Vacha et al.: Biomolecular simulations of membranes: Physical properties
from different force fields)
Only the Berger parameters reproduce approximately the membrane area per
lipid, order parameter, as Vlas wrote, and as far I know.
Balazs
Vlad Cojocaru wrote:
> Dear Adrian,
>
> At the moment I don't think there is any amber-compatible set of lipid
> parameters to be used in pure NPT simulations ...
> Of course, this would be the ideal case but most of the all-atom ff
> that I am aware of have the same problem .. I don't think its only an
> AMBER problem
>
> Although I thought about it ...I don't know the solution to this.. I
> guess its a study on its own ...
>
> The old united-atoms ff (Berger) do not have the problem with the area
> per lipid but seem to have other problems. I did not use them personally
> And there is the compatibility issue if one wants to do
> protein-membrane simulations with all-atom proteins
>
> Vlad
>
>
> Adrian Roitberg wrote:
>> Dear Balazs !
>>
>> Thanks I just read your paper, which I had on a pile anyways.
>>
>> Now, the conclusions you have is that it works as long as you add the
>> external surface tension.
>>
>>
>> As you discuss in the paper, I believe one should not need that extra
>> term, and a simple constant pressure simulations should find its
>> optimal area per lipid.
>>
>> Amber does not have a surface tension term, so I am trying to as: is
>> there a good set of parameters for popc that gives you the correct
>> area per lipid and order parameters WITHOUT needing a surface tension
>> term ?
>>
>> Please let me know if you guys have thought about this and what your
>> ideas are.
>>
>> Thanks !
>>
>>
>> On 3/31/10 10:56 AM, Balazs Jojart wrote:
>>> Dear Adrian,
>>> My name is Balazs Jojart, and we are the authors of the JCompChem
>>> article:
>>> Performance of the general amber force field in modeling aqueous POPC
>>> membrane bilayers.
>>> Cheers,
>>> Balazs
>>>
>>> Adrian Roitberg wrote:
>>>> Dear all,
>>>>
>>>> I am looking for one or two people that have tried and succeeded in
>>>> modeling membranes (DMPC, POOC, DOPC) using amber.
>>>>
>>>> Please answer off line to me if you can, so I can ask some questions.
>>>>
>>>> Thanks !
>>>>
>>>> Adrian
>>>>
>>>
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
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Received on Wed Mar 31 2010 - 09:30:04 PDT
