[gmx-users] CHARMM36 lipid bilayers

Thomas Piggot t.piggot at soton.ac.uk
Thu Oct 21 17:47:21 CEST 2010

Hi Sven,

I have also seen similar things from the area per lipid of the bilayers
I have run (POPC and DPPC). I would suggest you try running with the
CHARMM TIP3P water (tips3p.itp) and see if you get values which are
closer to the ones published in the paper you mention. This will be
discussed in a paper which we hope to have published fairly soon.



Sven Jakobtorweihen wrote:
> 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

Dr Thomas Piggot
University of Southampton, UK.

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