Thank you for your help. I checked all the force field, all of them are with default non-bond params in LJ. So I still need to try new solution. I add my non bond parameters in the .top file generated. Force field files were not changed. Then I use grompp, the error was:
'[ nonbond_params ]' Invalid order for directive nonbond_params Rather confused by setting up Buckingham potential parameters... Thank you very much! 2009/2/26 Berk Hess <g...@hotmail.com> > Hi, > > But do you need any other parameters than zinc and oxide? > If not, you can simply remove all other parameters. > If you need other atoms as well, you will need to find > a consistent force field, probably or completely LJ > or completely Buckingham. > > Berk > > > Date: Thu, 26 Feb 2009 09:22:26 +1100 > > From: mark.abra...@anu.edu.au > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] combination rules -- the part > aboutthecombinationrules > > > > Shuangxing Dai wrote: > > > Yes, "add parameters for crystalline zinc oxide, which require > > > Buckingham nonbonded interactions", that is what I am doing. I think I > > > have changed all the necessary parts for the Buckingham potential. Is > > > there any direct way to accomplish my goal? > > > > No, because it's not a reasonable goal. Your new atomtypes are talking a > > different vdW "language". That doesn't work. > > > > > Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type > > > > is 1. I only changed the parameters for Zn and O to Buckingham > > > parameters. And you said "add your functions in the right form in your > [ > > > molecule ] section" , I cannot find the right place to change. > > > > Chapter 5 of the manual. > > > > > And what > > > force field to choose if not ffgmx? > > > > That's your homework I'm afraid. You'll have to read the literature. > > > > Mark > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Shuangxing Dai
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php