I am running some replica runs of a simulation already done beforehand. In the previous simulations, some 54k water was used while solvating the structure. However, my box uses 53k spce water to solvate the system. The simulations are identical,uses all same parameters and the same starting structures. Someone pointed out the problem can be in the spc216.gro; hence I opened it and saw that it mentions SPC-MODEL. Kindly point me toward the issue here, is it a possibility that the previous sims used a different water structure file to solvate?
Several years ago, the values of atomic radii were updated, which changes how tools like gmx solvate perceives clashes and decides which atoms to remove. This may explain the difference, but the previous simulations would have had to have been performed with a pretty old version of GROMACS for this to be the case (pre-5.0, IIRC).
The difference isn’t due to the coordinate file itself, unless the old systems were prepared with a non-standard version of spc216.gro (e.g. something not provided by GROMACS).