Hi I ran a md simulation for a system with two groups: Surrounding , LIG. I wish to set the charges of the surrounding group to zero and to recalculate the Coulomb interactions between the groups. For this purpose I used tpbconv with the -zeroq option:
tpbconv_d -s md_prev.tpr -f md_prev.trr -n -o md_new.tpr -zeroq and I selected the surrounding group as the group that will be "zeroed". next I ran a rerun: mdrun_d -nt 8 -v -deffnm md_new -rerun md_prev.xtc after the rerun finished I used g_energy to analyze the results: g_energy_d -f md_new.edr -o md_new.xvg The Coul-SR:Surrounding-Surrounding was 0 as expected and so was Coul-SR:Surrounding-LIG the problem is that also Coul-SR:LIG-LIG was also 0 (and the same for the LR values). Could anyone please help me understand why this happened? Thank you very much Yocheved
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