Dear gmx users,
Imagine it's a protein-membrane system which GROMOS53a6 and CHARMM36 will give
me the same acceptable output for it. Now if I want to choose one, what am I
supposed to chose? How can I have a good option? Any suggestion? Or any
articles available?
I guess the CHARMM FF is good because it would give me results in details, but
is time consuming!
Thanks for your suggestions in advance.
Sincerely,
Shima
________________________________
From: Thomas Piggot <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Wednesday, May 16, 2012 5:55 PM
Subject: Re: [gmx-users] forcefields for lipids
Hi,
In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger, OPLS-AA)
there are several united-atom GROMOS based lipid forcefields (43A1-S3,
53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a useful place to find
lots of lipid parameters in one location:
http://lipidbook.bioch.ox.ac.uk/
The choice of force field will depend upon what you wish to simulate. With PC
lipids there are more force fields available compared to other phospholipids,
so your choice of lipid may dictate your choice of force field. Additionally
some of the available lipid force fields may work well for one type of lipid
but not another. Finally if you have a membrane-protein system you also need to
consider the combination with an appropriate protein force field.
Cheers
Tom
Peter C. Lai wrote:
> Off the top of my head:
> There are the Berger lipids for the gromos FFs (Justin's tutorial)
> There was a B2
Adrenergic receptor paper that used Amber.
> and of course Martini appears to be everyone's favorite coarse grain FF.
>
> The literature search shall be left as an exercise for the reader.
> (You can even use google to search this mailing list or mirrors of it)
>
> On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote:
>> Dear gmx users,
>>
>> Which force fields are suggested for lipids? Except CHARMM, any other
>> forcefields?
>> Anybody may suggest me articles in this about?
>>
>>
>> Thanks in advance
>>
>> Sincerely,
>> Shima
>
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>
>
-- Dr Thomas Piggot
University of Southampton, UK.
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