[gmx-users] Pre-equilibrated CHARMM lipid bilayers

[Joakim Jämbeck]

We have performed relatively long simulations of a WALP23 peptide embedded in DLPC and DOPC bilayers with different flavors of the Amber FF family. Currently I am working with much bigger protein and see good agreement between the simulations and experiments.

You could probably use those bilayers with CHARMM, just make sure you equilibrate a while before just to be safe.

Best,
Joakim



On Dec 19, 2012, at 19:22 , gmx-users-request at gromacs.org wrote:

> Date: Wed, 19 Dec 2012 18:45:33 +0300
> From: James Starlight <jmsstarlight at gmail.com>
> Subject: Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<CAALQopyMeJ=g7LrgJ+n2PDsEo_fW77xZhR38b4eAFJmam06odQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Joakim!
> 
> MAny thanks for such big collection of the bilayers. Have your
> simulated different protein embedded in that bilayers ? What force
> field did you use for parametrisation of the proteins for such
> simulations ? From the mdp file I noticed relatively big cutoffs for
> vdw as well as electrostatics ( bigger than in charmm force fields).
> Would it possible to simulate proteins parametrized by charmm in that
> lipids ussing charmm parametres for whole system?
> 
> 
> Thanks again,
> 
> James