Thanks for the suggestion. I tried it, but for my system the gain is not significant.
I was aware that it is preferable to remove the centre-of-mass for each leaflet separately. However, in my tests, I removed the center-of-mass of the membrane because I intent to simulate peptide-membrane interactions. In such case, the center-of-mass of the protein-membrane system is usually removed. Is their any way to remove the CoM motion of each leaflet separately on one hand, and peptide-membrane system CoM motion on the other? Thanks, Sebastien ---------------------------------------- > Date: Fri, 3 Aug 2012 11:10:22 -0400 > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? > From: da...@cornell.edu > To: gmx-users@gromacs.org > > Hello, > > I ran into similar issues for a DPPC bilayer. It might be possible > that the two leaflets of the bilayer are moving with respect to > eachother. If this is not taken into account, these artificial > velocities will mean the simulation thinks it is at a higher > temperature than it really is. If possible, you might want to try > subtracting the center of mass motion of each leaflet, rather than the > center of mass motion of the entire bilayer. This will allow the > system to equillibrate to the correct (higher) temperature, and should > increase the area per lipid of the bilayer. > > Hope this helps. > -David > > On Thu, Aug 2, 2012 at 8:22 AM, Sebastien Cote > <sebastien.cot...@umontreal.ca> wrote: > > > > > > Dear Gromacs users, > > > > I did new tests on the POPE membrane with CHARMM36 parameters, but I still > > always get area per lipid values that are smaller than experimental value > > by 4 to 6 Angstrom2. Here are my new tests. > > > > My initial configuration is an equilibrated POPE membrane with 80 lipids at > > 1 atm and 310K in NPT. It was taken from Klauda's website and it was > > obtained from the study in which the POPE parameters were tested (Klauda, > > J. B. et al. 2010 J. Phys. Chem. B, 114, 7830-7843). > > > > I use TIPS3P (Charmm's special TIP3P). My simulations parameters are > > similar to those used in a previous tread on the Gromacs mailing list > > (http://lists.gromacs.org/pipermail/gmx-users/2010-October/055161.html for > > DMPC, POPC and DPPC of 128 lipids each) : > > > > dt = 0.002 ps; rlist = 1.0 nm; rlistlong = 1.4 nm; coulombtype = pme; > > rcoulomb = 1.4 nm; vdwtype = switch or cutoff (see below); DispCorr = No; > > fourierspacing = 0.15 nm; pme_order = 6; tcoupl = nose-hoover; tau_t = 1.0 > > ps; ref_t = 310K; pcoupl = Parrinello-Rahman; pcoupltype = semiisotropic; > > tau_p = 5.0 ps; compressibility = 4.5e-5; ref_p = 1.0 atm; constraints = > > h-bonds; constraint_algorithm = LINCS. Nochargegrps was used when executing > > pdb2gmx. > > > > The simulation time of each simulation is 100 ns. I tried different VdW > > cutoff values, since it was previously mentioned that cutoff values for VdW > > may influence the area per lipid. The average value and standard deviation > > are calculated on the 20 to 100 ns time interval. > > > > 1- For VdW switch from 0.8 to 1.2 nm : The area per lipid is 54.8 +/- 1.6 > > A2. > > 2- For VdW switch from 1.1 to 1.2 nm : The area per lipid is 54.6 +/- 1.8 > > A2. > > 3- For VdW cutoff at 1.4 nm : The area per lipid is 55.9 +/- 1.6 A2. > > > > I also checked the influence of DispCorr with VdW switch from 0.8 to 1.2 nm > > : > > > > 1- Without DispCorr : The area per lipid is 54.8 +/- 1.6 A2. > > 2- With DispCorr : The area per lipid is 54.4 +/- 1.9 A2. > > > > I also checked the influence of PME cutoff with VdW switch from 0.8 to 1.2 > > nm : > > > > 1- For PME cutoff at 1.4 nm : The area per lipid is 54.8 +/- 1.6 A2. > > 2- For PME cutoff at 1.0 nm : The area per lipid is 56.4 +/- 1.5 A2. > > > > These values are smaller than 4-6 A2 when compared against the experimental > > value (59.75-60.75 A2) and the value obtained in Klauda's simulation (59.2 > > +/- 0.3 A2). DispCorr and LJ cutoff weakly impact the results. Reducing the > > PME cutoff seems to have the greatest effect, but the value obtained is > > still smaller than experimental value by 3-4 A2. > > > > I also tried other initial configurations, but the results were either very > > similar or worst. > > > > Larger membrane gave similar results for the mean values and smaller > > standard deviations. > > > > ------- > > > > Have anyone else tried to simulate a CHARMM36 POPE membrane in Gromacs? Do > > you get similar results? > > > > Is a 3-4 A2 deviation from experiment likely to influence my > > membrane/peptide simulations? Would it then be preferable to go with > > CHARMM27 in the NPAT ensemble? > > > > At this point, I have no clue of how to reproduce correctly Klauda's > > results for POPE. Any suggestion is welcomed. > > > > Thanks, > > > > Sebastien > > > > > > ---------------------------------------- > > > Date: Mon, 23 Jul 2012 16:06:40 -0500 > > > From: p...@uab.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? > > > > > > On 2012-07-23 02:34:31PM -0300, Sebastien Cote wrote: > > > > > > > > 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. > > > > > > I alwasy thought it was actually forcefield dependent. I never use it with > > > CHARMM since the mdp files I used as the basis for mine didn't with C27, > > > and > > > I get acceptable APL with POPC when using the same mdp with C36. I haven't > > > compared the codes for CHARMM to see if dispcorr is builtin to the gromacs > > > implementation or not, but the reason I brought it up is that on past > > > mailing list discussions about TIPS3P, there were reports of significant > > > density differences with and without dispcorr. > > > > > > > > > > > > > > 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? 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