[gmx-users] CHARMM36 lipid bilayers
t.piggot at soton.ac.uk
Fri Oct 22 11:51:30 CEST 2010
Yes I have tested values of rvdw-switch and (unlike in your test) have
seen a large impact of the area per lipid. Indeed this can also be seen
in the Klauda paper where they show a decreased area per lipid (~63 A^2
to ~58 A^2) in the NAMD DPPC simulations (see the graph in the
Supporting Info) using a 1.1 nm cut-off for the switching compared to
the 0.8 nm cut-off in their CHARMM simulations.
I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM
tip3p water. This gives me the closest results in terms of area per
lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM
results) and experiment.
Sven Jakobtorweihen wrote:
> Hi there,
> Tom, thanks for this hint, yes, that is an improvement. I am looking
> forward to your paper. Berk, I am using switch for vdw. Although for my
> taste switching from 0.8 to 1.2 was quite large, I used it because the
> charmm paper used these values. But I just realized that the
> implementation of the switch is different in gromacs and charmm, I
> should have seen that earlier. I think I will increase rvdw_switch to
> 1.0. However, a couple of days ago I tested already the influence of the
> switching region and it wasn't dramatic, at least for the test case.
> Nevertheless, matching the settings used in the parametrization is
> always advisable. Tom, do you have tested any cutoff settings?
> Berk Hess schrieb:
>> 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
>>>> 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
>>>> 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
>>>> have suggestions how to improve it? Are these differences expected
>>>> comparing gromacs and charmm simulations? Did by any chance
>> someone else
>>>> tested charmm36 bilayers in gromacs?
>>> Dr Thomas Piggot
>>> University of Southampton, UK.
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Dr Thomas Piggot
University of Southampton, UK.
More information about the gromacs.org_gmx-users