[gmx-users] running solvate twice...

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Tue Dec 9 09:27:20 CET 2014


Dear Justin,

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

This really shouldn't happen.  How are you adding these additional waters?  If it's via -ci -nmol, then I can understand there is some ability for individual molecules to find voids that might not be present when simply solvating with -cs, but there is nothing at all suspicious about the density obtained in step 1.

 I used -cs spc216.gro

I would have thought the density should be 1000 or slightly higher, not lower.

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

Further driving things in the wrong direction.  Moreover, I don't think it proves anything you happen to be able to flood in waters in one snapshot of a longer simulation.  Voids come and go that may accommodate waters as things move around, but that doesn't mean you need to fill them.  Unless your box is behaving in some bizarre way such that there are obvious, large voids, I don't see any purpose to doing all of these solvating steps.

All the solvate runs I described in my previous email were only to try and trouble-shoot the issue.  If you think 1 round of solvate is fine, I'm quite happy to leave off the second round.




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


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

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