Re: [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.pig...@soton.ac.uk>
*To:* Discussion list for GROMACS users <gmx-users@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.pig...@soton.ac.uk 
<mailto:t.pig...@soton.ac.uk>>
 > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org 
<mailto:gmx-users@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-requ...@gromacs.org 
<mailto:gmx-users-requ...@gromacs.org> 
<mailto:gmx-users-requ...@gromacs.org 
<mailto:gmx-users-requ...@gromacs.org>> wrote:
 >  >
 >  >> Date: Tue, 22 May 2012 13:49:48 +0100
 >  >> From: Thomas Piggot <t.pig...@soton.ac.uk 
<mailto:t.pig...@soton.ac.uk> <mailto:t.pig...@soton.ac.uk 
<mailto:t.pig...@soton.ac.uk>>>
 >  >> Subject: Re: [gmx-users] forcefields for lipids
 >  >> To: Discussion list for GROMACS users <gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>>>
 >  >> Message-ID: <4fbb8b6c.70...@soton.ac.uk 
<mailto:4fbb8b6c.70...@soton.ac.uk> <mailto:4fbb8b6c.70...@soton.ac.uk 
<mailto:4fbb8b6c.70...@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.
 > --
 > gmx-users mailing list    gmx-users@gromacs.org 
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-- Dr Thomas Piggot
University of Southampton, UK.
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--
Dr Thomas Piggot
University of Southampton, UK.
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