[gmx-users] Re: solvation

[Jamie Seyed]

Hi Justin,
Thank you very much. I did not know that...
On Thu, Aug 13, 2009 at 8:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
>
> --
> ========================================
>
> 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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