Hi, You have very strange and complex cut-off settings in Gromacs. What Charmm settings are you trying to mimic?
Berk > Date: Thu, 21 Oct 2010 15:03:51 +0200 > From: jakobtorwei...@tuhh.de > To: gmx-users@gromacs.org > Subject: [gmx-users] CHARMM36 lipid bilayers > > 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 > -- > 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
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