On 12/6/12 8:22 PM, Nur Syafiqah Abdul Ghani wrote:
Dear Users,
May I know after do the command
genbox -cp prot_box.gro -ci solvent.gro -nmol 2000 -cs spc216.gro -p
control.top -o prot_mix_sol.gro
the result shows,
Output configuration contains 1121788 atoms in 367835 residues
Volume : 11420.4 (nm^3)
Density : 1007.84 (g/l)
Number of SOL molecules: 365793
I need to put the solvent mix with water with ratio approximately 80%
of solvent : 20% water.
From here after i done the calculation its only give 5% of solvent in water.
Therefore my question is,can i add another -nmol of solvent without
insert the -cs anymore?
Hope you guys already facing the same problem like i do.
The best approach is to do it in two steps:
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
-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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