[gmx-users] gmx solvate density problem

Justin Lemkul jalemkul at vt.edu
Fri Mar 25 12:49:04 CET 2016

On 3/24/16 2:41 PM, Irem Altan wrote:
> Hi,
> I am trying to add tip4p water into the unit cell of a protein. I have removed the crystal waters. The output of gmx solvate is the following:
> Output configuration contains 4642 atoms in 753 residues
> Volume                 :     38.4496 (nm^3)
> Density                :      1223.1 (g/l)
> Number of SOL molecules:    603
> I have not changed the vdW radii. Why could the density be this high? How is the solvent volume estimated anyway?

It's an approximate density based on assumptions about atom names, etc.  It's 
relatively meaningless, as you'll need to equilibrate anyway.



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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