Hi there, Tom, many thanks for your valuable suggestions. I am also surprised by this large influence. For DPPC the change is about 5 A^2 (same settings but different water model).
Cheers, Sven Pär Bjelkmar schrieb: > I'm a bit surprised that the CHARMM tip3p makes a significant > difference, how large is the difference approximately? > > /Pär > >> Hi Sven, >> >> 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. >> >> Cheers >> >> Tom >> >> 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? >>> >>> Cheers, >>> Sven >>> >>> Berk Hess schrieb: >>>> Hi, >>>> >>>> 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. >>>> >>>> Berk >>>> >>>>> Date: Thu, 21 Oct 2010 16:47:21 +0100 >>>>> From: t.pig...@soton.ac.uk <mailto:t.pig...@soton.ac.uk> >>>>> To: gmx-users@gromacs.org <mailto:gmx-users@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. >>>>> >>>>> Cheers >>>>> >>>>> Tom >>>>> >>>>> 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. >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto:gmx-users@gromacs.org> >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> 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-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org>. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> -- >> Dr Thomas Piggot >> University of Southampton, UK. > > > <><><><><><><><><><><><><><><><><><><><><> > > Pär Bjelkmar, Ph.D. student > > > Stockholm Center for Biomembrane Research (CBR), > > Stockholm Bioinformatics Center (SBC), > > Department of Biochemistry and Biophysics (DBB), > > Stockholm University > > > Tel: +46-8-16 2746 > > Fax: +46-8-15 3679 > > E-mail: bjelk...@cbr.su.se <mailto:bjelk...@cbr.su.se> > > Home: http://www.dbb.su.se/User:Bjelkmar > > <><><><><><><><><><><><><><><><><><><><><> > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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. 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