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
