[gmx-users] solvent molecules do not fill up the entire box

Maziya Ibrahim maziya.ibrahim at gmail.com
Sat Jul 26 14:08:24 CEST 2014

I have used the following to solvate the protein:

editconf -f complex.gro -o newbox.gro -center 3.5 5.5 5 -box 17 11 10

genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top

The topology file is updated with 60841 solvent molecules added to the

""Initialising van der waals distances...
Will generate new solvent configuration of 10x6x6 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 77760 residues
Calculating Overlap...
box_margin = 0.315
Removed 34434 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Grid: 40 x 26 x 23 cells
Successfully made neighbourlist
nri = 288956, nrj = 7794234
Checking Protein-Solvent overlap: tested 52677 pairs, removed 3726 atoms.
Checking Solvent-Solvent overlap: tested 1193220 pairs, removed 12597 atoms.
Added 60841 molecules
Generated solvent containing 182523 atoms in 60841 residues
Writing generated configuration to solv1.gro
Protein in water

Output configuration contains 184981 atoms in 61087 residues
Volume                 :        1870 (nm^3)
Density                :     1004.74 (g/l)
Number of SOL molecules:  60841   ""

But on visualizing the solv.gro file in VMD it appears that the solvent
molecules are situated only at one end of the box as seen in this pic --

How do I make it such that the solvent is evenly distributed?

[image: http://oi62.tinypic.com/2vkgi8l.jpg]

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