[gmx-users] CHARMM36 lipid bilayers

[Berk Hess]

Hi,

You have very strange and complex cut-off settings in Gromacs.
What Charmm settings are you trying to mimic?

Berk

> Date: Thu, 21 Oct 2010 15:03:51 +0200
> From: Jakobtorweihen at tuhh.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] CHARMM36 lipid bilayers
> 
> Dear gmx-users,
> 
> recently Pär Bjelkmar and Thomas Piggot have generated force field files
> for Charmm36 lipids. I run some simulations to find the best run
> parameters and to check if the results of the original Charmm36 lipid
> article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
> reproduced with gromacs.
> 
> I run 40 ns NPT simulations with semiisotropic pressure coupling
> (Parrinello-Rahman, tau_p=5),  the first 10 ns are equilibration and
> averages were calculated for the last 30 ns. DMPC and POPC at 303 K and
> DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with
> pdb2gmx -nochargegrp. All simulations contained 128 lipids and
> approximately the same water/lipid ratio (water is TIP3P) as Klauda et
> al. I started from charmm27 bilayers provided at the Chramm Gui website.
> I used the following parameters:
> 
>  rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
> rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;
> nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002
> 
> These simulations result in the following area per lipid [A^2/lipid]:
> DMPC=56.6 +/- 0.4  ; POPC =61.8 +/- 0.4 ;  DPPC=55.0 +/- 0.7
> 
> Comparing to the results of Klauda et al (all simulation with the
> charmm-package, except one):
> DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
> +/- 0.4 (with NAMD)
> 
> It is obvious that my simulations with gromacs 4.5.1 give lower areas
> per lipid for all cases. Considering the deviations observed by Klauda
> et al. between Charmm and NAMD simulations ( rvdw_switch was only
> changed slightly in NAMD) could lead to the conclusion that DMPC and
> POPC are fine. But I am a bit worried about the DPPC result. Did anyone
> have suggestions how to improve it? Are these differences expected when
> comparing gromacs and charmm simulations? Did by any chance someone else
> tested charmm36 bilayers in gromacs?
> 
> Thanks,
> Sven
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