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