[gmx-users] forcefields for lipids

[Thomas Piggot]

Hi,

In my opinion the choice of force field will depend upon exactly what 
you are simulating and why you are simulating it. Different force fields 
(both lipid and protein) have their own advantages and disadvantages and 
so it is really up to you to decide this (after doing some background 
reading about different force fields).

Additionally you may wish to use more than one force field to run repeat 
simulations to verify what you see in your simulations, if this is 
feasible to do.

Cheers

Tom

Shima Arasteh wrote:
> 
>  I'm going to simulate the protein in  POPC bilayer. Do you suggest this 
> forcefield for this kind of bilayer too?
> Thanks so much for your reply.
> Sincerely,
> Shima
> ------------------------------------------------------------------------
> *From:* Thomas Piggot <t.piggot at soton.ac.uk>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, May 22, 2012 10:15 PM
> *Subject:* Re: [gmx-users] forcefields for lipids
> 
> Hi Shima,
> 
> Yes, the phospholipid parameters are available to use. I am currently in 
> the process of uploading them to the Lipidbook website. If you check 
> this website soon they should be available to download (DPPE and POPE 
> parameters and bilayers are already there). For accessing them on 
> Lipidbook the name of the force field is the GROMOS-CKP lipid force 
> field. The parameters are consistent for use with the GROMOS 53A6 and 
> GROMOS 54A7 protein force fields for simulating membrane proteins 
> systems. I should also note that the Kukol DMPC and DPPC parameters 
> (http://pubs.acs.org/doi/abs/10.1021/ct8003468) are also consistent with 
> these phospholipid parameters, if you wish to simulate mixed lipid bilayers.
> 
> Cheers
> 
> Tom
> 
> Shima Arasteh wrote:
>  > Is this FF available for others to use?
>  >
>  > Thanks.
>  >  Sincerely,
>  > Shima
>  > ------------------------------------------------------------------------
>  > *From:* Thomas Piggot <t.piggot at soton.ac.uk 
> <mailto:t.piggot at soton.ac.uk>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
>  > *Sent:* Tuesday, May 22, 2012 7:39 PM
>  > *Subject:* Re: [gmx-users] forcefields for lipids
>  >
>  > Thanks Joakim,
>  >
>  > I will be very interested to see how these different lipids behave. 
> This looks like it could be a really useful force field. We have also 
> developed some parameters for PE, PG and Cardiolipin lipids which you 
> might want to have a look at (for comparison with your ongoing parameter 
> development). Details regarding the behaviour of these lipids are in the 
> supporting info of this paper 
> (http://pubs.acs.org/doi/abs/10.1021/jp207013v).
>  >
>  > Cheers
>  >
>  > Tom
>  >
>  > Joakim Jämbeck wrote:
>  >  > Hi Tom,
>  >  >
>  >  > we have parameters for unsaturated tails now as well as for PE 
> lipids ready for use, the manuscript for these have been submitted.
>  >  >
>  >  > PG and PS lipids are on the way and parameters for cholesterol and 
> sphingomyelin are finished now and the manuscript should be finished 
> relatively soon.
>  >  >
>  >  > Best,
>  >  > J
>  >  >
>  >  >
>  >  > On May 22, 2012, at 15:40 , gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org> 
> <mailto:gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>> wrote:
>  >  >
>  >  >> Date: Tue, 22 May 2012 13:49:48 +0100
>  >  >> From: Thomas Piggot <t.piggot at soton.ac.uk 
> <mailto:t.piggot at soton.ac.uk> <mailto:t.piggot at soton.ac.uk 
> <mailto:t.piggot at soton.ac.uk>>>
>  >  >> Subject: Re: [gmx-users] forcefields for lipids
>  >  >> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>>
>  >  >> Message-ID: <4FBB8B6C.70101 at soton.ac.uk 
> <mailto:4FBB8B6C.70101 at soton.ac.uk> <mailto:4FBB8B6C.70101 at soton.ac.uk 
> <mailto:4FBB8B6C.70101 at soton.ac.uk>>>
>  >  >> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>  >  >>
>  >  >> Hi Joakim,
>  >  >>
>  >  >> I am interested to know what other lipids this force field has 
> been extended to include. Do you have parameters for unsaturated lipid 
> tails and other classes of phospholipid (such as PE and PG)?
>  >  >>
>  >  >> Cheers
>  >  >>
>  >  >> Tom
>  >
>  > -- Dr Thomas Piggot
>  > University of Southampton, UK.
>  > --
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> 
> -- Dr Thomas Piggot
> University of Southampton, UK.
> --
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-- 
Dr Thomas Piggot
University of Southampton, UK.