On 1/23/18 9:29 AM, za...@tezu.ernet.in wrote:
Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: SDS initial setup (Dallas Warren) 2. Is there any difference with gromacs and other MD programs? (??? (?????)) 3. MDP define in GROMACS 2018 (Joshua Mitchell) 4. Cannot find position restraint file restraint.gro (Sailesh Bataju) ---------------------------------------------------------------------- Message: 1 Date: Mon, 22 Jan 2018 11:42:51 +1100 From: Dallas Warren <dallas.war...@monash.edu> To: GROMACS users <gmx-us...@gromacs.org> Subject: Re: [gmx-users] SDS initial setup Message-ID: <CAOv1qzaVWjsEmxSO+GZf3YZBOF8LZU4=qsrbbo6fhm2jz0d...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8"Thank you Justin and Dallas for your kind response. PBC comes into effect from the start of minimization step. As we apply it in the minim.mdp file as pbc = xyz. However in my case the SDS molecules appears to be outside during initial setup itself. Kindly correct me if I missed out something.
What you might be missing is that there is no such thing as "outside" of a periodic box. You are looking at the central image of an infinite system, so the molecules are always surrounded by images of the particles across the boundaries.
However if that is the case, it might sounds vague but I am thinking why then we center the protein (eg and keep it 1 nm from the edge of the box to its center) during protein setup?
Convenience. You need to define a size for the central image that satisfies the minimum image convention, so we position our solute(s) of interest in the center of that image (which again is an arbitrary definition when considering an infinite number of representations) and compute a box size based on the resulting solute coordinates that will provide a suitable buffer to satisfy the MIC.
-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.
