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 >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. 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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.