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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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