[gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins

[Ollila Samuli]

Hi,

I used ffgmx.itp. It contains CB.

BR,
Samuli Ollila

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of David Ackerman [da294 at cornell.edu]
Sent: Wednesday, May 07, 2014 10:30 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins

Thank you for your advice.

Which force field was used? I have downloaded the cholesterol parameters
from Höltje et al, but atomtypes like CB do not exist in the force field I
am using (53a6). Did you change these to other atomtypes as well, or were
you using a force field that included them?

-David


On Wed, May 7, 2014 at 8:59 AM, Ollila Samuli <samuli.ollila at aalto.fi>wrote:

> Hi,
>
> In my understanding the CH2-LP2 attraction is stronger than LP2-LP2
> attraction in the Berger/Höltje combination you described. If you then have
> CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too
> condensed bilayer. I think that the related issue is discussed here:
>
> http://dx.doi.org/10.1088/0953-8984/18/28/S07
>
> and here:
>
> http://dx.doi.org/10.1039/C2CP42738A
>
> we have changed the CH2 groups in cholesterol to LP2 groups and compared
> the results quite extensively to the NMR measurements.
>
> BR,
> Samuli Ollila
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of David
> Ackerman [da294 at cornell.edu]
> Sent: Monday, May 05, 2014 7:39 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol
>       and Proteins
>
> Hello,
>
> I have been performing simulations of multi-component bilayers using
> parameters described in the following paper:
> http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield
> with Berger lipid parameters included. They also use cholesterol from
> Holtje et. al (
> http://www.sciencedirect.com/science/article/pii/S000527360100270X), which
> was parameterized for the ffgmx force field.
>
> I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting
> the default lipid-gromos Berger interactions, the authors kept those
> interactions in the force field. In light of newer force fields, are these
> older force fields wither Berger parameters still acceptable? The
> cholesterol model seems commonly used, so I am unsure how to use
> cholesterol with a newer force field.
>
> Furthermore, if I were to include proteins in the simulation, would I still
> be able to use the same ffgmx force field with Berger parameters (including
> lipid-gromos interactions)?
>
> Thank you,
> David
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