Dear Peter, Did you use any different simulation conditions for your POPC membrane? I tried many different ones for POPE, without never reproducing Klauda's results. I may try yours on my POPE membrane.
In my simulations, I want to study peptide-membrane interactions. The peptide is not embedded in the membrane. It is initially completely solvated without any interactions with the membrane. Then, I want to look at its adsorption and degree of insertion in the membrane. For that system, I can not remove the CoM motion of the protein alone, otherwise it will not adsorb and insert in the membrane. I may try (as you suggested) to remove CoM of the bottom leaflet on one hand, and the peptide-upperleaflet on the other hand. My peptide is not very long (17 to 35 amino acids), so I believe that remove the CoM of the peptide-upperleaflet/bottomleaflet will not have any pernicious effect. What do you think? Thanks for the suggestion, Sébastien ---------------------------------------- > Date: Wed, 8 Aug 2012 20:19:56 -0500 > From: p...@uab.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? > > Personally, I could remove the COM of each leaflet when equilibrating the > bilayer by itself (and as a side note I am not experiencing a similar problem > with POPC that you're having with POPE...). However, after the protein is > embedded, I have gotten good results for my protein, which extends from the > water through the entire membrane into more water, by using a whole System > COM removal. The introduction of my particular embedded protein acts as a > physical coupling between the water layers with the lipids (not to mention if > I choose to model the lipid raft localization crosslink, it will have to > happen anyway). If your protein doesn't extend fully past both layers of the > membrane you may want to stick with just coupling a Membrane+Protein+1 layer > of water or Membrane+Protein and Water separately (like in Justin's KALP15 > tutorial). You will have to decide what you think is physically realistic > based on the interaction between the water, membrane, and protein when the > protein is embedded. (if your protein is assymetrically embedded you may even > use the following COM groups: protein+involved leaflet, second leaflet, > water). > > On 2012-08-09 09:38:01AM +1000, Mark Abraham wrote: > > On 9/08/2012 3:28 AM, Sebastien Cote wrote: > > > 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? > > > > See 7.3.3 of manual. > > > > Mark > > > > > > > > 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? 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. 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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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. 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. 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists