On Tue, Oct 4, 2011 at 2:57 AM, elisa carli <elisacarl...@gmail.com> wrote:
> Hi Lisa > Thank you very much for your reply. > After minimimization could I run a molecular dynamic production? > Or have I to do other sets? > Yes, after energy minimization, you need do some other sets (like NVT and NPT). Could you write me which are the commands to execute up to MD run? > The links Justin provided are very useful. It's not a bad idea to do some tutor to be familiar with those procedures. > > Bests > > 2011/9/22 lina <lina.lastn...@gmail.com> > >> On Thu, Sep 22, 2011 at 11:34 AM, elisa carli <elisacarl...@gmail.com>wrote: >> >>> Dear All >>> >>> I'd like to perfom a MD simulation on a membrane protein using DLPC or >>> DPPC system >>> I've downloaded the API package from this link >>> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies >>> >>> DPPC.zip and DLPC.zip by schiu >>> >>> How can I use them? Where can I get a tutorial or commands illustrating >>> the use of these packages? >>> >>> Thanks in advance >>> >> Here is a rough procedure: >> >> http://www.nanoconductor.org/43A1-S3/ >> >> Took Chiu's DPPC.zip as an example. We use the speptide.pdb peptide from >> the gromacs tutorial (it's a bad choice to put it in the dppc, but we just >> try it). >> >> pdb2gmx_g -f speptide.pdb -o speptide.gro >> >> choose >> 9: GROMOS96 43a1 force field >> 1: SPC simple point charge, recommended >> >> $ tail -1 dppc.gro >> 5.68585 5.60685 6.85739 >> >> To be as simple as possible here, we use the dimension of the dppc.gro >> >> editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2 >> -box 5.68585 5.60685 6.85739 >> >> now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by >> >> genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top >> >> >> Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide, >> >> the purpose of doing a simple energy minimization here just want to "test" >> the topol.top. >> >> it used 43A1-S3 force field (You can download from >> http://www.nanoconductor.org/43A1-S3/). >> >> The head of topol.top: >> ; Include forcefield parameters >> #include "ffG43A1-S3.itp" >> #include "lipids_43A1-S3.itp" >> >> The tail of topol.top: >> >> [ molecules ] >> ; Compound #mols >> Protein 1 >> DPPC 71 >> SOL 3205 >> >> I manually added DPPC 71. >> >> please copy the lipids_43A1-S3.itp ffG43A1-S3.itp >> ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current >> directory, >> extra copy ff_dum.itp from >> some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working >> directory. >> >> I attached all those files in try.tar.gz >> >> https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB >> >> mdrun_g -v -deffnm em >> >> works well. >> >> >> -- >> Best Regards, >> >> lina >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> 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 > 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 > -- Best Regards, lina
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