On 3/18/13 2:56 PM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to obtain given density for my system for a given molecule
- its a cubic box of 5 nm in dimension.
I calculated that I need 850 molecules to get the density of 500 g/mol
In my box there is already 1 molecule so I try:
genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb
Added 819 molecules (out of 849 requested)
Output configuration contains 9020 atoms in 820 residues
Volume : 125 (nm^3)
Density : 480.336 (g/l)
Number of SOL molecules: 0
How can I add 30 more molecules using gromacs? I want to avoid adding
it manually.
Use a larger box and equilibrate. All genbox tries to do is add molecules
randomly, which is not a foolproof process. If the force field parameters
indeed produce the correct density, you should be able to produce it rather quickly.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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