[gmx-users] forcefields for lipids
shima_arasteh2001 at yahoo.com
Fri May 18 14:47:07 CEST 2012
Dear gmx users,
Imagine it's a protein-membrane system which GROMOS53a6 and CHARMM36 will give me the same acceptable output for a protein-membrane system. 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.
From: Thomas Piggot <t.piggot at soton.ac.uk>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, May 16, 2012 5:55 PM
Subject: Re: [gmx-users] forcefields for lipids
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:
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.
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
>> -- gmx-users mailing list gmx-users at gromacs.org
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-- Dr Thomas Piggot
University of Southampton, UK.
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