I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far.
I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder. There may well be other ways to do this but I haven't found them yet. On 3 Dec 2013 10:14, panzu <sergio.panzu...@estudiante.uam.es> wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. ----- Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
