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 >>>> To: 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 >>>> 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. >>>> 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 Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><><><><>
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