Sorry about that. I didn't see that in the inbox. Excuse me...
What am I thinking about are some notes in the tutorial. For example

>The above command centers the protein in the box (-c), and places it at least 
>1.0 nm from the box >edge (-d 1.0). The box type is defined as a cube (-bt 

So, can I make a bigger problem by setting that to 4.0 nm? What about other box 

>[ molecules ]
>; Compound      #mols
>Protein_A         1
>SOL           10824
>CL                8

I see 8 green points in the figure in that page. Can I increase that to put 
more molecules in the cube?
What are the blue dots in the figure? Are they atoms? If I want to increase the 
number of atoms, should I use another pdb file and run pdb2gmx again?

>; Name       nrexcl
>Protein_A    3

Can I blindly increase that 3?

Can I use another pdb file (other than 1AKI) and follow the same procedure? 

Generally, the type of my questions are like those.


On Tuesday, March 13, 2018, 2:48:35 PM GMT+3:30, Justin Lemkul 
<> wrote: 

On 3/13/18 2:49 AM, Mahmood Naderan wrote:
> No idea? Any feedback is appreciated.

You likely missed my reply:



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061 | (540) 231-3129


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