Dear Felipe, I will take a lot at this paper.
Thanks! Sebastien ---------------------------------------- > Date: Tue, 4 Aug 012 9::8::7 +200< > From: luis.pinedadecas...@lnu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] CHARMM6 - Smaller Area per lipid for POPE - Why? > > Hi Sébastien, > > I found the following paper very instructive about this issue (simulated > areas per lipid in bilayers): > > Jensen, M. et al. Simulations of a membrane anchored peptide: structure, > dynamics, and influence on bilayer properties. Biophys. J. (004))6,, 556--5< > > Take maybe a look at it, if you haven't done it already. > > Regards, > > Felipe > > On 8//3//012 1::2 PM, Peter C. Lai wrote: > > Oh something I didn't mention: for bond constraints I used h-bonds instead > > of all-bonds. This may or may not make a difference (although I switched to > > h-bonds based on the suggestion of some charmm/lipid thread on here from > > a couple of years ago). > > > > On 012--8--9 2::4::9PPM -300,, Sebastien Cote wrote: > >> 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 (7 to 5 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, Aug 012 0::9::6 -500< > >>> From: p...@uab.edu > >>> To: gmx-users@gromacs.org > >>> Subject: Re: [gmx-users] CHARMM6 - 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+ > >>> layer > >>> of water or Membrane+Protein and Water separately (like in Justin's KALP5< > >>> 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 012--8--9 9::8::1AAM +000,, Mark Abraham wrote: > >>>> On //8//012 ::8 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 .... of manual. > >>>> > >>>> Mark > >>>> > >>>>> Thanks, > >>>>> > >>>>> Sebastien > >>>>> > >>>>> ---------------------------------------- > >>>>>> Date: Fri, Aug 012 1::0::2 -400< > >>>>>> Subject: Re: [gmx-users] CHARMM6 - Smaller Area per lipid for POPE - > >>>>>> Why? > >>>>>> From: da94@@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 ,, 012 at ::2 AM, Sebastien Cote > >>>>>> <sebastien.cote.@@umontreal.ca> wrote: > >>>>>>> Dear Gromacs users, > >>>>>>> > >>>>>>> I did new tests on the POPE membrane with CHARMM6 parameters, but I > >>>>>>> still always get area per lipid values that are smaller than > >>>>>>> experimental value by to Angstrom.. Here are my new tests. > >>>>>>> > >>>>>>> My initial configuration is an equilibrated POPE membrane with 0 > >>>>>>> lipids at atm and 10KK 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. 010 J. Phys. Chem. B, 14,, 830--843)). > >>>>>>> > >>>>>>> I use TIPSPP (Charmm's special TIPPP). My simulations parameters are > >>>>>>> similar to those used in a previous tread on the Gromacs mailing list > >>>>>>> (http://lists.gromacs.org/pipermail/gmx-users/010--October/55161..html > >>>>>>> for DMPC, POPC and DPPC of 28 lipids each) : > >>>>>>> > >>>>>>> dt = ..02 ps; rlist = .. nm; rlistlong = .. nm; coulombtype = pme; > >>>>>>> rcoulomb = .. nm; vdwtype = switch or cutoff (see below); DispCorr = > >>>>>>> No; fourierspacing = ..5 nm; pme_order = ;; tcoupl = nose-hoover; > >>>>>>> tau_t = .. ps; ref_t = 10KK; pcoupl = Parrinello-Rahman; pcoupltype = > >>>>>>> semiisotropic; tau_p = .. ps; compressibility = ..ee-;; ref_p = .. > >>>>>>> atm; constraints = h-bonds; constraint_algorithm = LINCS. > >>>>>>> Nochargegrps was used when executing pdbggmx. > >>>>>>> > >>>>>>> The simulation time of each simulation is 00 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 0 to 00 ns time interval. > >>>>>>> > >>>>>>> -- For VdW switch from .. to .. nm : The area per lipid is 4.. +/- .. > >>>>>>> A.. > >>>>>>> -- For VdW switch from .. to .. nm : The area per lipid is 4.. +/- .. > >>>>>>> A.. > >>>>>>> -- For VdW cutoff at .. nm : The area per lipid is 5.. +/- .. A.. > >>>>>>> > >>>>>>> I also checked the influence of DispCorr with VdW switch from .. to > >>>>>>> .. nm : > >>>>>>> > >>>>>>> -- Without DispCorr : The area per lipid is 4.. +/- .. A.. > >>>>>>> -- With DispCorr : The area per lipid is 4.. +/- .. A.. > >>>>>>> > >>>>>>> I also checked the influence of PME cutoff with VdW switch from .. to > >>>>>>> .. nm : > >>>>>>> > >>>>>>> -- For PME cutoff at .. nm : The area per lipid is 4.. +/- .. A.. > >>>>>>> -- For PME cutoff at .. nm : The area per lipid is 6.. +/- .. A.. > >>>>>>> > >>>>>>> These values are smaller than -- A when compared against the > >>>>>>> experimental value (9..5--0..5 A)) and the value obtained in Klauda's > >>>>>>> simulation (9.. +/- .. A)). 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 -- > >>>>>>> A.. > >>>>>>> > >>>>>>> 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 CHARMM6 POPE membrane in > >>>>>>> Gromacs? Do you get similar results? > >>>>>>> > >>>>>>> Is a -- A deviation from experiment likely to influence my > >>>>>>> membrane/peptide simulations? Would it then be preferable to go with > >>>>>>> CHARMM7 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, 3 Jul 012 6::6::0 -500< > >>>>>>>> From: p...@uab.edu > >>>>>>>> To: gmx-users@gromacs.org > >>>>>>>> Subject: Re: [gmx-users] CHARMM6 - Smaller Area per lipid for POPE - > >>>>>>>> Why? > >>>>>>>> > >>>>>>>> On 012--7--3 2::4::1PPM -300,, 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 .. > >>>>>>>>> to .. 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 > >>>>>>>> C7,, and > >>>>>>>> I get acceptable APL with POPC when using the same mdp with C6.. 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 TIPSPP, there were reports of > >>>>>>>> significant > >>>>>>>> density differences with and without dispcorr. > >>>>>>>> > >>>>>>>> > >>>>>>>>> Thanks, > >>>>>>>>> > >>>>>>>>> Sebastien > >>>>>>>>> > >>>>>>>>> ---------------------------------------- > >>>>>>>>>> Date: Fri, 0 Jul 012 2::7::4 -500< > >>>>>>>>>> From: p...@uab.edu > >>>>>>>>>> To: gmx-users@gromacs.org > >>>>>>>>>> Subject: Re: [gmx-users] CHARMM6 - Smaller Area per lipid for POPE > >>>>>>>>>> - Why? > >>>>>>>>>> > >>>>>>>>>> Did you play with DispCorr? > >>>>>>>>>> > >>>>>>>>>> On 012--7--0 9::6::3AAM -300,, Sebastien Cote wrote: > >>>>>>>>>>> Dear Gromacs users, > >>>>>>>>>>> > >>>>>>>>>>> My simulations on a POPE membrane using the CHARMM6 parameters > >>>>>>>>>>> are giving ''area per lipid'' values well below the experimental > >>>>>>>>>>> value (9..5--0..5 Angstroms)). Is their someone else experiencing > >>>>>>>>>>> a similar problem? If yes, how did you solved it? > >>>>>>>>>>> > >>>>>>>>>>> I did the following : > >>>>>>>>>>> > >>>>>>>>>>> I used the CHARMM6 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 0 lipids equilibrated in NPT at T=10KK > >>>>>>>>>>> and P=aatm for 0 ns. It is taken from the article Klauda, J. B. > >>>>>>>>>>> et al. 010 J. Phys. Chem. B, 14,, 830--843.. > >>>>>>>>>>> > >>>>>>>>>>> At first, I tested normal TIPPP vs. CHARMM TIPPP and saw that > >>>>>>>>>>> normal TIPPP gives smaller Area per lipid of about -- Angstroms. > >>>>>>>>>>> This was also observed by T.J. Piggot (personnal communication) > >>>>>>>>>>> and Tieleman (Sapay, N. et al. 010 J. Comp. Chem. 2,, 400--410)). > >>>>>>>>>>> So, I will present only the simulations using CHARMM TIPPP. As in > >>>>>>>>>>> Klauda's paper, my simulations are at 10KK and atm. As them, I > >>>>>>>>>>> used a switch cutoff for vdw, and I used normal cutoff for PME. > >>>>>>>>>>> The simulations are 0 ns. I can send my .mdp file for more > >>>>>>>>>>> details. I varied the switch condition on vdw : > >>>>>>>>>>> > >>>>>>>>>>> -- For a switch from .. to .. (as in Klauda's paper), I got Area > >>>>>>>>>>> per lipid of about 6.. Angstroms;; whereas they got 9.. in their > >>>>>>>>>>> paper, matching the experimental value of 9..5--0..5.. > >>>>>>>>>>> -- For a switch from .. to ..,, I got Area per lipid of about 3.. > >>>>>>>>>>> Angstroms,, 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. > >>>>>>>>>>> -- For a switch from .. to ..,, I got Area per lipid of about 5 > >>>>>>>>>>> Angstroms.. > >>>>>>>>>>> -- For a hard cutoff at ..,, I got Area per lipid of about 2 > >>>>>>>>>>> Angstroms.. > >>>>>>>>>>> > >>>>>>>>>>> I also tried to re-equilibrate the membrane in the NPAT ensemble > >>>>>>>>>>> for 0 ns at 10KK and atm. Then, when I launched the simulation in > >>>>>>>>>>> NPT, I ended up with different results : > >>>>>>>>>>> > >>>>>>>>>>> -- Switch from .. to .. gave a smaller area per lipid of 4 > >>>>>>>>>>> Angstroms.. > >>>>>>>>>>> -- Switch from .. to .. gave a larger area per lipid of 5 > >>>>>>>>>>> Angstroms.. > >>>>>>>>>>> -- Hard cutoff at .. gave a similar area per lipid of 2.. > >>>>>>>>>>> Angstroms.. > >>>>>>>>>>> > >>>>>>>>>>> I looked at the POPE paramaters for CHARMM6 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 CHARMM7 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 -- 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
