[gmx-users] computation/memory modifications
nt_mahmood at yahoo.com
Tue Mar 13 14:50:28 CET 2018
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?
>[ molecules ]
>; Compound #mols
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
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 <jalemkul at vt.edu> 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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