Hello, Greetings from Pawan. Giving the command and the options being used will be much better to give any further probable suggestions. Just using " -np 4 " wont solve the problem as such. You should specify the " -pname " option also. You can use NA+ ions to neutralize the system as its having negative charge. And when specifying the -np or -nn option u need not use -neural option.
Regards, Pawan On Fri, May 22, 2009 at 4:30 PM, Stefano Meliga <smel...@gmail.com> wrote: > Thanks Pawan, > > I added 4 positive ions as you suggested but the system total charge > reported in genion.log is still -4! > > Why? > > Cheers, > > Stefano > > > Pawan Kumar ha scritto: > >> Hello, >> >> Greetings from Pawan. >> -np is a parameter used to add the nmber of positive ions. >> when u have -4 negative charge u should give -np 4. >> -np with -pname will be more appropriate. >> see through this website for the proper usage of genion options. >> http://www.gromacs.org/documentation/reference_3.3/online/genion.html >> >> Regards, >> Pawan >> On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga <smel...@gmail.com<mailto: >> smel...@gmail.com>> wrote: >> >> Dear all, >> >> As the on-screen output of grompp says, my system has non-zero >> total charge = -4.000 >> >> Thus, I'm trying to neutralize the system using genion with this >> command line: >> >> genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p >> 4AKEallHsol_pre.top -neutral >> >> The problem is that the on-screen output says: >> >> "No ions to add and no potential to calculate" >> as the system was already neutral, I guess. >> >> I then tryied with the command line: >> >> genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p >> 4AKEallHsol_pre.top -neutral -np 50 -g >> >> Ions are added to the SOL group but the total charge remains -4, >> as the log file says. >> >> Do you know the reason? >> >> Thanks a lot, >> >> Stefano >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > _______________________________________________ > 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 >
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