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Hi,<br><br>Another comment on your interaction settings.<br>You did not mail if you are using shift or switch for vdw.<br>But I guess that both probably don't match exactly what Charmm does.<br>Since the switching range is so long and this is where a large part<br>of the dispersion attraction acts, this might have a large effect on the area.<br><br>Berk<br><br>> Date: Thu, 21 Oct 2010 16:47:21 +0100<br>> From: t.piggot@soton.ac.uk<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] CHARMM36 lipid bilayers<br>> <br>> Hi Sven,<br>> <br>> I have also seen similar things from the area per lipid of the bilayers<br>> I have run (POPC and DPPC). I would suggest you try running with the<br>> CHARMM TIP3P water (tips3p.itp) and see if you get values which are<br>> closer to the ones published in the paper you mention. This will be<br>> discussed in a paper which we hope to have published fairly soon.<br>> <br>> Cheers<br>> <br>> Tom<br>> <br>> Sven Jakobtorweihen wrote:<br>> > Dear gmx-users,<br>> > <br>> > recently Pär Bjelkmar and Thomas Piggot have generated force field files<br>> > for Charmm36 lipids. I run some simulations to find the best run<br>> > parameters and to check if the results of the original Charmm36 lipid<br>> > article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be<br>> > reproduced with gromacs.<br>> > <br>> > I run 40 ns NPT simulations with semiisotropic pressure coupling<br>> > (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and<br>> > averages were calculated for the last 30 ns. DMPC and POPC at 303 K and<br>> > DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with<br>> > pdb2gmx -nochargegrp. All simulations contained 128 lipids and<br>> > approximately the same water/lipid ratio (water is TIP3P) as Klauda et<br>> > al. I started from charmm27 bilayers provided at the Chramm Gui website.<br>> > I used the following parameters:<br>> > <br>> > rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;<br>> > rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;<br>> > nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002<br>> > <br>> > These simulations result in the following area per lipid [A^2/lipid]:<br>> > DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7<br>> > <br>> > Comparing to the results of Klauda et al (all simulation with the<br>> > charmm-package, except one):<br>> > DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1<br>> > +/- 0.4 (with NAMD)<br>> > <br>> > It is obvious that my simulations with gromacs 4.5.1 give lower areas<br>> > per lipid for all cases. Considering the deviations observed by Klauda<br>> > et al. between Charmm and NAMD simulations ( rvdw_switch was only<br>> > changed slightly in NAMD) could lead to the conclusion that DMPC and<br>> > POPC are fine. But I am a bit worried about the DPPC result. Did anyone<br>> > have suggestions how to improve it? Are these differences expected when<br>> > comparing gromacs and charmm simulations? Did by any chance someone else<br>> > tested charmm36 bilayers in gromacs?<br>> > <br>> > Thanks,<br>> > Sven<br>> <br>> -- <br>> Dr Thomas Piggot<br>> University of Southampton, UK.<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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