Hi, all:
I was trying to use "tpbconv" to modify the tpr file with the command:
tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr
It basically sets the charge of one group to zero. However, when I
perform mdrun -rerun, all the coulombic energies are zeros, i.e.,
Coulomb-(SR), Coul.-recip. This really does not make sense since I
still have atoms in other groups that are charged. I was using
gromacs4.0.7.
Has anyone seen this before? What exactly is the correct way to
zeroize the charge for a group of atoms?
Thanks,
Bin
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