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Thank you very much for your answers. Anyway, if I want to simulate my protein with Amber, would it be a big problem to combine parameter from Amber with parameters from OPLS for water and/or ions?<BR>
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Best wishes,<BR>
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Rebeca.<BR> <BR>> Date: Tue, 2 Jun 2009 09:51:12 -0300<BR>> Subject: Re: [gmx-users] crystals of KCl during simulation<BR>> From: moura@ufscar.br<BR>> To: gmx-users@gromacs.org<BR>> <BR>> Hi Rebeca,<BR>> <BR>> the paper David suggests is certainly more complete, I just compared OPLS<BR>> and Aqvist's parameters for sodium for the specific case of anionic<BR>> micelles. anyway, if want to try the Aqvist's parameters take a look<BR>> inside ffoplsaa.atp file (opls_408 for K+).<BR>> <BR>> best regards,<BR>> <BR>> André<BR>> <BR>> > Rebeca García Fandiño wrote:<BR>> >><BR>> >> Thank you very much, André. Could you please indicate me how could<BR>> >> I use these parameters in Gromacs? I have not seen them included in<BR>> >> ions.itp and I could not find anything in the manual.<BR>> >> Best wishes,<BR>> >> Rebeca.<BR>> ><BR>> ><BR>> > I would recommend reading the following paper, even though it only is<BR>> > about NaCl it compares the properties of four different parameter sets,<BR>> > and IIRC Åqvist's parameters were not so great.<BR>> ><BR>> > @Article{ Hess2006c,<BR>> > author = "B. Hess and C. Holm and N. {van der Vegt}",<BR>> > title = "Osmotic coefficients of atomistic NaCl (aq) force<BR>> > fields",<BR>> > journal = "J. Chem. Phys.",<BR>> > year = 2006,<BR>> > volume = 124,<BR>> > pages = 164509,<BR>> > abstract = "Solvated ions are becoming increasingly important<BR>> > for (bio)molecular simulations. But there are not<BR>> > much suitable data to validate the<BR>> > intermediate-range solution structure that ion-water<BR>> > force fields produce. We compare six selected<BR>> > combinations of four biomolecular Na-Cl force fields<BR>> > and four popular water models by means of effective<BR>> > ion-ion potentials. First we derive an effective<BR>> > potential at high dilution from simulations of two<BR>> > ions in explicit water. At higher ionic<BR>> > concentration multibody effects will become<BR>> > important. We propose to capture those by employing<BR>> > a concentration dependent dielectric<BR>> > permittivity. With the so obtained effective<BR>> > potentials we then perform implicit solvent<BR>> > simulations. We demonstrate that our effective<BR>> > potentials accurately reproduce ion-ion coordination<BR>> > numbers and the local structure. They allow us<BR>> > furthermore to calculate osmotic coefficients that<BR>> > can be directly compared with experimental data. We<BR>> > show that the osmotic coefficient is a sensitive and<BR>> > accurate measure for the effective ion-ion<BR>> > interactions and the intermediate-range structure of<BR>> > the solution. It is therefore a suitable and useful<BR>> > quantity for validating and parametrizing atomistic<BR>> > ion-water force fields. (c) 2006 American Institute<BR>> > of Physics. 0021-9606"<BR>> > }<BR>> ><BR>> ><BR>> ><BR>> >><BR>> >><BR>> >> > Date: Mon, 1 Jun 2009 14:52:35 -0300<BR>> >> > Subject: RE: [gmx-users] crystals of KCl during simulation<BR>> >> > From: moura@ufscar.br<BR>> >> > To: gmx-users@gromacs.org<BR>> >> ><BR>> >> > Hi Rebeca,<BR>> >> ><BR>> >> > I found out a few years ago that OPLS parameters for Na+ were<BR>> >> inadequate<BR>> >> > for my simulations on surfactants aggregation due to the formation of<BR>> >> > stable (and unrealistic) ionic bridges. I got better structures using<BR>> >> > Aqvist's parameters (available in GROMACS), maybe you could try these<BR>> >> > parameters for K+ as well.<BR>> >> ><BR>> >> > please let me know if that works.<BR>> >> ><BR>> >> > best regards,<BR>> >> ><BR>> >> > André<BR>> >> ><BR>> >> ><BR>> >> > ><BR>> >> > > Yes, I use PME.<BR>> >> > ><BR>> >> > >> Date: Mon, 1 Jun 2009 19:34:27 +0200<BR>> >> > >> From: spoel@xray.bmc.uu.se<BR>> >> > >> To: gmx-users@gromacs.org<BR>> >> > >> Subject: Re: [gmx-users] crystals of KCl during simulation<BR>> >> > >><BR>> >> > >> Rebeca García Fandiño wrote:<BR>> >> > >> > Thank you very much for your answer. I have read some recent<BR>> >> > >> literature,<BR>> >> > >> > and you are right, it is a problem about the parameters for ions<BR>> >> in<BR>> >> > >> Amber.<BR>> >> > >> ><BR>> >> > >> > I have found this paper:<BR>> >> > >> > Parameters of Monovalent Ions in the Amber-99 Forcefield:<BR>> >> Assesment of<BR>> >> > >> > Inaccuracies and Proposed Improvements<BR>> >> > >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392<BR>> >> > >> ><BR>> >> > >> > There, they simulate nucleic acids using a combination of Amber<BR>> >> and<BR>> >> > >> > OPLS sigma and epsilon for the ions. I have tried that in the<BR>> >> case of<BR>> >> > >> my<BR>> >> > >> > protein, just changing the ion sigma and epsilon in the topology<BR>> >> by<BR>> >> > >> > those corresponding to OPLS, but I still observe aggregation for<BR>> >> the<BR>> >> > >> ions.<BR>> >> > >> ><BR>> >> > >> > Would this combination of Amber and OPLS have any kind of<BR>> >> potential<BR>> >> > >> > problem during the simulation? Has anybody any idea to avoid<BR>> >> this type<BR>> >> > >> > of artefact?<BR>> >> > >><BR>> >> > >> Just checking, do you use PME? (You should...)<BR>> >> > >> ><BR>> >> > >> > Thank you very much in advance,<BR>> >> > >> ><BR>> >> > >> > Rebeca.<BR>> >> > >> ><BR>> >> > >> > > To: gmx-users@gromacs.org<BR>> >> > >> > > Subject: Re: [gmx-users] crystals of KCl during simulation<BR>> >> > >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200<BR>> >> > >> > > From: baaden@smplinux.de<BR>> >> > >> > ><BR>> >> > >> > ><BR>> >> > >> > > Hi,<BR>> >> > >> > ><BR>> >> > >> > > regafan@hotmail.com said:<BR>> >> > >> > > >> [..] but after equilibration I have observed that KCl is<BR>> >> > >> > aggregating, like<BR>> >> > >> > > >> if it was making crystals. When I used NaCl instead KCl,<BR>> >> this not<BR>> >> > >> > > >> happened.<BR>> >> > >> > ><BR>> >> > >> > > >> Does anybody has any idea about the reason of the behaviour<BR>> >> of<BR>> >> > >> KCl in<BR>> >> > >> > > >> the simulation?<BR>> >> > >> > ><BR>> >> > >> > > This even does happen with Amber :) So my guess is you<BR>> >> correctly<BR>> >> > >> > transferred<BR>> >> > >> > > the parameters, but stumbled upon an artefact. If you check<BR>> >> the<BR>> >> > >> recent<BR>> >> > >> > > literature you may notice that many publications with Amber<BR>> >> using K+<BR>> >> > >> > > only employ minimal (neutralising) salt conditions as a<BR>> >> workaround.<BR>> >> > >> At<BR>> >> > >> > > least this is what we did recently [1].<BR>> >> > >> > ><BR>> >> > >> > > Marc Baaden<BR>> >> > >> > ><BR>> >> > >> > > [1] Interactions between neuronal fusion proteins explored by<BR>> >> > >> molecular<BR>> >> > >> > > dynamics, Biophys.J.94, 2008, 3436-3446.<BR>> >> > >> > > http://dx.doi.org/10.1529/biophysj.107.123117<BR>> >> > >> > ><BR>> >> > >> > > --<BR>> >> > >> > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris<BR>> >> > >> > > mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr<BR>> >> > >> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217<BR>> >> > >> > ><BR>> >> > >> > ><BR>> >> > >> > > _______________________________________________<BR>> >> > >> > > gmx-users mailing list gmx-users@gromacs.org<BR>> >> > >> > > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> >> > >> > > Please search the archive at http://www.gromacs.org/search<BR>> >> before<BR>> >> > >> > posting!<BR>> >> > >> > > Please don't post (un)subscribe requests to the list. Use the<BR>> >> > >> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> >> > >> > > Can't post? Read<BR>> >> http://www.gromacs.org/mailing_lists/users.php<BR>> >> > >> ><BR>> >> > >> ><BR>> >> ------------------------------------------------------------------------<BR>> >> > >> > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en<BR>> >> la<BR>> >> > >> Zona<BR>> >> > >> > Fan de MSN Deportes<BR>> >> > >> > <http://opiniones.msn.es/default.aspx/Futbol/Atletico-de-Madrid<BR>> >> ><BR>> >> > >> ><BR>> >> > >> ><BR>> >> > >> ><BR>> >> ------------------------------------------------------------------------<BR>> >> > >> ><BR>> >> > >> > _______________________________________________<BR>> >> > >> > gmx-users mailing list gmx-users@gromacs.org<BR>> >> > >> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> >> > >> > Please search the archive at http://www.gromacs.org/search<BR>> >> before<BR>> >> > >> posting!<BR>> >> > >> > Please don't post (un)subscribe requests to the list. Use the<BR>> >> > >> > www interface or send it to gmx-users-request@gromacs.org.<BR>> >> > >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> >> > >><BR>> >> > >><BR>> >> > >> --<BR>> >> > >> David.<BR>> >> > >><BR>> >> ________________________________________________________________________<BR>> >> > >> David van der Spoel, PhD, Professor of Biology<BR>> >> > >> Dept. of Cell and Molecular Biology, Uppsala University.<BR>> >> > >> Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>> >> > >> phone: 46 18 471 4205 fax: 46 18 511 755<BR>> >> > >> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>> >> > >><BR>> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>> >> > >> _______________________________________________<BR>> >> > >> gmx-users mailing list gmx-users@gromacs.org<BR>> >> > >> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> >> > >> Please search the archive at http://www.gromacs.org/search before<BR>> >> > >> posting!<BR>> >> > >> Please don't post (un)subscribe requests to the list. Use the<BR>> >> > >> www interface or send it to gmx-users-request@gromacs.org.<BR>> >> > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> >> > ><BR>> >> > > _________________________________________________________________<BR>> >> > > Recibe toda las noticias de actualidad al instante en tu Messenger<BR>> >> > > http://especiales.es.msn.com/noticias/msninforma.aspx<BR>> >> > > _______________________________________________<BR>> >> > > gmx-users mailing list gmx-users@gromacs.org<BR>> >> > > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> >> > > Please search the archive at http://www.gromacs.org/search before<BR>> >> posting!<BR>> >> > > Please don't post (un)subscribe requests to the list. Use the<BR>> >> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> >> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> >> ><BR>> >> ><BR>> >> > _______________________________________________<BR>> >> > gmx-users mailing list gmx-users@gromacs.org<BR>> >> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> >> > Please search the archive at http://www.gromacs.org/search before<BR>> >> posting!<BR>> >> > Please don't post (un)subscribe requests to the list. Use the<BR>> >> > www interface or send it to gmx-users-request@gromacs.org.<BR>> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> >><BR>> >> ------------------------------------------------------------------------<BR>> >> El nuevo Windows Live tiene mucho que ofrecerte. Descúbrelo en estos<BR>> >> vídeos <http://www.windowslive.es ><BR>> >><BR>> >><BR>> >> ------------------------------------------------------------------------<BR>> >><BR>> >> _______________________________________________<BR>> >> gmx-users mailing list gmx-users@gromacs.org<BR>> >> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> >> Please search the archive at http://www.gromacs.org/search before<BR>> >> posting!<BR>> >> Please don't post (un)subscribe requests to the list. Use the<BR>> >> www interface or send it to gmx-users-request@gromacs.org.<BR>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> ><BR>> ><BR>> > --<BR>> > David.<BR>> > ________________________________________________________________________<BR>> > David van der Spoel, PhD, Professor of Biology<BR>> > Dept. of Cell and Molecular Biology, Uppsala University.<BR>> > Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>> > phone: 46 18 471 4205 fax: 46 18 511 755<BR>> > spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>> > _______________________________________________<BR>> > gmx-users mailing list gmx-users@gromacs.org<BR>> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > Please search the archive at http://www.gromacs.org/search before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the<BR>> > www interface or send it to gmx-users-request@gromacs.org.<BR>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> ><BR>> ><BR>> <BR>> <BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><br /><hr />Disfruta antes que nadie del nuevo <a href='http://download.live.com' target='_new'>Windows Live Messenger</a></body>
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