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 2012-08-09 12:34:19PM -0300, 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 
> (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
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> > > >>>>>> --
> > > >>>>>> ==================================================================
> > > >>>>>> 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 |
> > > >>>>>> ==================================================================
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> > > >>>> 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
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> > ==================================================================
> > 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
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==================================================================
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                  |
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