[gmx-users] CHARMM36 lipid bilayers
gmx3 at hotmail.com
Fri Oct 22 09:33:47 CEST 2010
Another comment on your interaction settings.
You did not mail if you are using shift or switch for vdw.
But I guess that both probably don't match exactly what Charmm does.
Since the switching range is so long and this is where a large part
of the dispersion attraction acts, this might have a large effect on the area.
> Date: Thu, 21 Oct 2010 16:47:21 +0100
> From: t.piggot at soton.ac.uk
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] CHARMM36 lipid bilayers
> 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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