[gmx-users] running solvate twice...

Justin Lemkul jalemkul at vt.edu
Mon Dec 8 13:38:39 CET 2014

On 12/8/14 4:24 AM, Harry Mark Greenblatt wrote:
> BS"D
> Dear All,
>    While setting up a system with a small DNA binding domain (30 residues) in close proximity to 9 bp of B DNA, in a dodecahedron box,
> I ran gmx solvate which added about 7,000 water molecules (spce), followed by addition of 0.125M NaCl.
> I then minimized this setup, and ran 100ps each of
> constant pressure equilibration and npt equilibration (basically following the spider toxin example).  Our group head then suggested I try
> and add water again, just to fill any gaps, if they exist.  This time gmx solvate added more than 600 water molecules, which is close
> to 10% of the total.
> This is rather alarming, or so we think...
> Comments?

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.

Using NPT should not allow voids to appear/persist, so multiple rounds of 
solvation does not make sense to me in the first place.  Bubbles can arise under 
NVT, although very infrequently for a "normal" system, but NPT would close them 



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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