[gmx-users] forcefields for lipids
shima_arasteh2001 at yahoo.com
Wed May 16 15:44:54 CEST 2012
Thanks for all your suggestions.
Honestly, I want to simulate a protein-membrane system. My chosen membrane is POPC. After the simulation of the system, I'm gonna apply the umbrella sampling on the system to study the ion conduction through the channel composed of this protein.
Before this, I had seen that the ion conduction through the gramicidin A channel in a bilayer were studied using CHARMM. Refer to that article I guess the CHARMM may give me the best out put. Is this an acceptable choice of a force field?
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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