[gmx-users] Adding Ions

errabah fatima ezzahra errabahf at yahoo.fr
Wed Jul 13 18:26:32 CEST 2011

Hi All,

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 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110713/2bea73ff/attachment.html>

More information about the gromacs.org_gmx-users mailing list