[gmx-users] add more solvent?

[Justin Lemkul]

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

-- 
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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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