On 3/13/18 9:50 AM, Mahmood Naderan wrote:
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 cubic)
So, can I make a bigger problem by setting that to 4.0 nm? What about other box 
types?

A cubic box is the least efficient, so to achieve your goal of a slower simulation, stick with a cube. Increasing the buffer size around the protein will lead to more waters being added.


[ 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?

The 8 Cl- ions balance the charge on the protein. Don't try to change this.

The blue atoms you see are water.


; Name       nrexcl
Protein_A    3
Can I blindly increase that 3?

No, because then you're going to start breaking the model physics, whether or not you care I don't know.

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

Generally, yes, but don't follow it exactly because the number of ions added depends on the charge on the protein.

-Justin

Generally, the type of my questions are like those.




Regards,
Mahmood







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





On 3/13/18 2:49 AM, Mahmood Naderan wrote:
No idea? Any feedback is appreciated.
You likely missed my reply:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119068.html

-Justin



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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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