[gmx-users] running solvate twice...

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Mon Dec 8 10:24:48 CET 2014


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...


Using Gromacs 5.0.2.




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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