[gmx-users] running solvate twice...

[Harry Mark Greenblatt]

BS"D

Dear Justin,



Yes, this is weird.  Where are the new waters added?  If they're at the periphery, there's probably just some incorrect accounting for PBC, in which case any subsequent run likely shouldn't be stable.


The new water molecules are scattered throughout the box.  The density of the system behaves in the following manner

1.  First run of solvate:   7025 waters added, density 994.192 g/l  (a bit low??)

2.  Run solvate on result of 1:  20 waters added, density  996.828 g/l

3.  Run solvate on result of 1 after adding ions and minimization:  171 waters added, density 1015.3 g/l

4.  Run solvate on result of 1 after adding ions, minimize, position restrained dynamics, npt dynamics:  636 waters added, density 1113.91 g/l

Harry




-------------------------------------------------------------------------

Harry M. Greenblatt

Associate Staff Scientist

Dept of Structural Biology

Weizmann Institute of Science        Phone:  972-8-934-3625

234 Herzl St.                        Facsimile:   972-8-934-4159

Rehovot, 76100

Israel


Harry.Greenblatt at weizmann.ac.il<mailto:Harry.Greenblatt at weizmann.ac.il>