[gmx-users] gmx solvate density problem

Irem Altan irem.altan at duke.edu
Thu Mar 24 19:41:08 CET 2016


I am trying to add tip4p water into the unit cell of a protein. I have removed the crystal waters. The output of gmx solvate is the following:

Output configuration contains 4642 atoms in 753 residues
Volume                 :     38.4496 (nm^3)
Density                :      1223.1 (g/l)
Number of SOL molecules:    603

I have not changed the vdW radii. Why could the density be this high? How is the solvent volume estimated anyway?


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