[gmx-users] Re: solvation

[Justin A. Lemkul]

Jamie Seyed wrote:

> my command is:
> genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 
> -nmol 1 -ci insert.gro
> I also tried
> genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 
> -nmol 1 -ci insert.gro -try 100
> by using 20,30,40...,100 but each time was the same. (I also did it 
> without shell command but no success)

You can't run -cs and -ci at the same time; they must be done in separate 
processes.  I would also get rid of -shell, in any case.  If you're filling the 
box with water, adding an additional shell of solvent has no effect.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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