[gmx-users] running solvate twice...

[Tsjerk Wassenaar]

Hey :)

Genbox takes account of VDW radii, if available. However, water is odd
stuff, building cages with hydrogen bonds, like clusters with ice-like
structure. My guess is that genbox considers these as cavities, based on
the VDW radii. Probably having around 10% 'hits' when overlaying another
water box is not even unreasonable. From the point of what genbox is
written for, I don't think it's wrong.

Cheers,

Tsjerk

On Tue, Dec 9, 2014 at 9:27 AM, Harry Mark Greenblatt <
harry.greenblatt at weizmann.ac.il> wrote:

> B"SD
>
> 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.
>
> Thanks
>
> 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>
>
>
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.