[gmx-users] How To SOLVATE

[Justin Lemkul]

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 
files, etc).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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