[gmx-users] How To SOLVATE
jalemkul at vt.edu
Mon Oct 28 02:41:00 CET 2013
On 10/27/13 9:30 PM, Hari Pandey wrote:
> 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.
genbox -maxsol 100 will put a block of no more than 100 waters in the unit cell.
genbox -ci -nmol 100 will add 100 molecules randomly within the unit cell.
> 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
There is a warning that masses may not be correctly detected for a reason. Are
you using any strange atoms? No one on this list can tell what is right without
seeing exactly what you're doing (description of the system, commands, input
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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