[gmx-users] Adding Ions
errabah fatima ezzahra
errabahf at yahoo.fr
Wed Jul 13 18:26:32 CEST 2011
I have a peptide that has three positive charged amino acids (LYS) and four negative charged amino acids (GLU) consequently it is a negative peptide. is that right
when i run gromacs simualtion grompp DOES NOT gave a warning:
System has non-zero total charge: -6 ( i have six peptides)
i tried neutralising the system, since that the peptides have an extra -1 charge per peptide.
however when i did add 6 NA to the system , after running the enrgy minimization there was an error that System has non-zero total charge: -6.000000e+00
so i dont understand how by adding 6 positive ions that cause the negative charge??
thank you so much for your help
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