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
