zakiya wrote: > Hi Gromacs users, > I have some problems about the total charge of system using Gromacs. > I wanted to perform a protein denaturation simulation induced by urea. At > first, I added urea molecules into the box including one CI2 protein. Then I > performed the energy minimization step. However, there’s a note that “NOTE 1 > [file ci2.top, line 3998]: System has non-zero total charge: 1.999878e+00 “. > My question is that why the total charge of system is not an integer. The > whole charge of CI2 protein is 2.000e+00.
Arithmetic on computers is subject to rounding errors after each operation. There are a number of threads on this list that have discussed this in the past. So long as the total charge is still close to an integer, you don't have evidence of a serious problem. See also http://oldwiki.gromacs.org/index.php/Errors#System_has_non-zero_total_charge Mark I got the ITP file of urea molecule from the “share” file in the Gromacs library directory. The total charge is zero. So this phenomena puzzled me. > The [atoms] field in the ITP file of urea molecule is as follows: > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > #ifdef Boek > 1 C 1 UREA C1 1 0.38 12.0110 > 2 O 1 UREA O2 1 -0.38 15.9994 > 3 NT 1 UREA N3 2 -0.83 14.0067 > 4 H 1 UREA H4 2 0.415 1.0080 > 5 H 1 UREA H5 2 0.415 1.0080 > 6 NT 1 UREA N6 3 -0.83 14.0067 > 7 H 1 UREA H7 3 0.415 1.0080 > 8 H 1 UREA H8 3 0.415 1.0080 > #else > 1 C 1 UREA C1 1 0.683 12.0110 > 2 O 1 UREA O2 1 -0.683 15.9994 > 3 NT 1 UREA N3 2 -0.622 14.0067 > 4 H 1 UREA H4 2 0.346 1.0080 > 5 H 1 UREA H5 2 0.276 1.0080 > 6 NT 1 UREA N6 3 -0.622 14.0067 > 7 H 1 UREA H7 3 0.346 1.0080 > 8 H 1 UREA H8 3 0.276 1.0080 > #endif > > Any help/suggestions will be greatly appreciated! > > Thank you!! > Na Zhang > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 _______________________________________________ gmx-users mailing list [email protected] http://lists.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
