[gmx-users] running solvate twice...

Justin Lemkul jalemkul at vt.edu
Mon Dec 8 20:19:16 CET 2014

On 12/8/14 8:59 AM, Harry Mark Greenblatt wrote:
> 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

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.

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

Even weirder.  How much space opened up after a simple minimization?  Again, I 
suppose this depends on how you're adding waters, but now you're forcing water 
in where it shouldn't be, because you have an abnormal density.

> 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.  It is indeed amazing 
that genbox can add so many waters, but it smells more of a bug than anything 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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