[gmx-users] How To SOLVATE

Hari Pandey harichem12 at yahoo.com
Mon Oct 28 02:30:54 CET 2013

Hi GROMACS users

can any body tell me how do I solvate fixed number of molecules in fixed volume: for example 100 molecule water in 14*14*14 Aungstrom^3  box.  eidt conf and genbox  never can do this.

One more question.
Please any body help me on following warning:

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Volume  of input 125 (nm^3)
Mass    of input 967.25 (a.m.u.)
Density of input 12.8493 (g/l)
Scaling all box vectors by 0.234221
new system size :  0.050  0.055  0.037
    shift       :  1.914  1.914  1.914 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00               (nm^3)

Here mass of input is not correct. It should be 444.5

Thanks in advance


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