Hi I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge?
Secondly, when I run a simulation of the same protein (7000 atoms) with certain restraints in vacuum, the simulation runs very slow. I am wondering why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. Using 4.5.3 -- Maria G. Technical University of Denmark Copenhagen
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