Hi, Can someone please provide me the link? I couldnt find the link in gromacs webpage related to these.also in wiki, this is not clearly described.
On Fri, Sep 5, 2008 at 2:47 AM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Thu, 4 Sep 2008 23:22:35 -0500 > "NAMD GROMACS" <[EMAIL PROTECTED]> wrote: > >> Hi, >> >> I have a couple of questions regarding top file and forcefield. >> >> 1st, in the top file >> >> [ angles ] >> ; ai aj ak funct c0 c1 c2 >> c3 >> 2 1 3 2 ga_9 >> 2 1 4 2 ga_9 >> 2 1 5 2 ga_10 >> 3 1 4 2 ga_9 >> 3 1 5 2 ga_10 >> Can you please tell me what the word "funct: stands for? what kind of >> functionals, why the numbers 2, and then in case of angles it changes to >> 1? >> I couldnt find good explanation for this in any manual or tutorial. >> > there is chapter dedicted to this ... and there the wiki (link at > www.gromacs.org) ... > > Also what does ga_9, ga_10 etc means..I guess the a in ga stands for angle, >> I dont know where the g is coming from. I am guessing the numbers are >> different types of bond. >> > you should have a look at the paper of the force field. > >> >> Question regarding the force-field. >> >> Select the Force Field: >> 0: GROMOS96 43a1 force field >> 1: GROMOS96 43b1 vacuum force field >> 2: GROMOS96 43a2 force field (improved alkane dihedrals) >> 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) >> 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) >> 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) >> 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) >> 7: [DEPRECATED] Gromacs force field (see manual) >> 8: [DEPRECATED] Gromacs force field with hydrogens for NMR >> 9: Encad all-atom force field, using scaled-down vacuum charges >> 10: Encad all-atom force field, using full solvent charges >> >> Here I am choosing 2 for my peptide in water run. I am wondering If I need >> to study peptide-mineral surface interaction, what number should I chose? >> Is >> there a way I can go beyond 10, or can I dvelop my own force field, .top >> file for interacting with mineral surface? Any suggestions on how to >> develop >> new .top file including metals and metal oxide surfaces would be also >> great >> help. >> >> Thanks >> >> Subhashis >> > > ----------------------------------------------------- > XAvier Periole - PhD > > Molecular Dynamics Group / NMR and Computation > University of Groningen > The Netherlands > ----------------------------------------------------- > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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