Dear Peter, I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as in Klauda's paper). I will retry with a more solvated membrane.
Would you have any thought on how the NPAT ensemble might affect peptide-membrane interactions like I am studying i.e. peptide is totally solvated, then adsorb, and finally may insert? The paper on peptide-membrane interaction like this usually use united-atom lipid in the NPT ensemble. Most of the work I have seen on Charmm membrane in the NPAT ensemble were for embedded membrane protein. Thanks, Sebastien ---------------------------------------- > Date: Mon, 13 Aug 2012 16:12:29 -0500 > From: p...@uab.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? > > 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 > > > > >>>>>>> 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? 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 > > > > > -- > > > > > 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 > > -- > ================================================================== > 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. 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