[gmx-users] Creating a box of water with density 1000 g/l
m.ebert at umontreal.ca
Thu Sep 10 22:46:42 CEST 2015
I am wondering if there is a better way to create a box with water of a certain size than:
gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512
To get a density of roughly 1000 g/l i would need to add 512 molecules in such a box. But the script only adds 502. I could play with the scale parameter but sometimes I have problems during minimization with messages like:
Water molecule starting at atom 1465 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Thank you very much,
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