There is not much difference when using DispCorr or not. At least on the same time scale as the simulation with switch cutoff from 0.8 to 1.2 nm and on the same time scale.
Should DispCorr be used in all membrane simulations? I thought that we should always use this correction. Thanks, Sebastien ---------------------------------------- > Date: Fri, 20 Jul 2012 12:47:44 -0500 > From: p...@uab.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? > > Did you play with DispCorr? > > On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote: > > > > Dear Gromacs users, > > > > My simulations on a POPE membrane using the CHARMM36 parameters are giving > > ''area per lipid'' values well below the experimental value (59.75-60.75 > > Angstroms2). Is their someone else experiencing a similar problem? If yes, > > how did you solved it? > > > > I did the following : > > > > I used the CHARMM36 parameters kindly provided by Thomas J. Piggot on the > > Users contribution section on Gromacs website. > > My starting configuration was taken from : > > http://terpconnect.umd.edu/~jbklauda/research/download.html > > It is a POPE membrane of 80 lipids equilibrated in NPT at T=310K and P=1atm > > for 40 ns. It is taken from the article Klauda, J. B. et al. 2010 J. Phys. > > Chem. B, 114, 7830-7843. > > > > At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that normal TIP3P > > gives smaller Area per lipid of about 2-3 Angstroms. This was also observed > > by T.J. Piggot (personnal communication) and Tieleman (Sapay, N. et al. > > 2010 J. Comp. Chem. 32, 1400-1410). So, I will present only the simulations > > using CHARMM TIP3P. As in Klauda's paper, my simulations are at 310K and 1 > > atm. As them, I used a switch cutoff for vdw, and I used normal cutoff for > > PME. The simulations are 20 ns. I can send my .mdp file for more details. I > > varied the switch condition on vdw : > > > > 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I got Area per > > lipid of about 56.5 Angstroms2; whereas they got 59.2 in their paper, > > matching the experimental value of 59.75-60.75. > > 2- For a switch from 1.0 to 1.2, I got Area per lipid of about 53.5 > > Angstroms2, which is smaller than the previous cutoff. This is surprising > > since a previous thread on gromacs-users mailing lists said that increasing > > the lower cutoff, increased the Area per lipid or had not impact on POPC of > > DPPC. > > 3- For a switch from 1.1 to 1.2, I got Area per lipid of about 55 > > Angstroms2. > > 4- For a hard cutoff at 1.4, I got Area per lipid of about 52 Angstroms2. > > > > I also tried to re-equilibrate the membrane in the NPAT ensemble for 10 ns > > at 310K and 1 atm. Then, when I launched the simulation in NPT, I ended up > > with different results : > > > > 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of 54 Angstroms2. > > 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55 Angstroms2. > > 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5 Angstroms2. > > > > I looked at the POPE paramaters for CHARMM36 in Gromacs, and they agree > > with the published parameters. > > > > Am I doing anything wrong? Is their someone else experiencing a similar > > problem for POPE? If yes, how did you solved it? > > > > Should I instead use CHARMM27 parameters in the NPAT ensemble? I want to > > study the interaction between a peptide and the POPE membrane. I am > > troubled that the NPAT ensemble might influence my results in a bad way. > > Also, I can not use OPLS AA nor GROMOS for the protein interactions because > > these force fields are not giving the correct structural ensemble for my > > peptide in solution. > > > > I am willing to send more information if you need. > > > > Thanks a lot, > > Sincerely, > > > > Sébastien -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * 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 > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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. 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