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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Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Wed Mar 31 2010 - 09:00:04 PDT
