Serdar. If the "real charge" of your system is not zero and you are using PME, then PME code will take account for any non-zero charge on the system and neutralize it with an uniform background charge ( http://wiki.gromacs.org/index.php/Errors). If your system is composed by a protein, then try first to check the charge for every residue (maybe you found some aminoacid with a not integral charge). Please note that several times if your charge is very close to an integer, this warning is generated as consequence of the " summation of many floating point numbers", check this link: http://www.gromacs.org/pipermail/gmx-users/2008-May/034092.html
However, your error is on the 3rd digit (by a magnitude of .004), on my experience gromacs "round errors" are very close to the integer (e.g. Sytem Charge = .9999998 or 1.000002), then I recommend you to take a look on your system. Daniel 2008/7/10 serdar durdagi <[EMAIL PROTECTED]>: > Dear all, > > > > In one of my simulations, total charge of the system is a noninteger number > (like +15.996). I neutralized it with 16 chlorine atoms. I am using periodic > boundary conditions. If I use the charge as it is, is it means infinite > negative total charge on the system? > > > > Actually, when I check the simulation output parameters, it seems every > thing okay..I am just curious if it's some thing wrong.. > > > > Serdar > > ------------------------------ > Gesendet von Yahoo! > Mail<http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52427/*http://de.overview.mail.yahoo.com>. > > Dem pfiffigeren Posteingang. > > _______________________________________________ > 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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