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 <[email protected]> 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 [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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