Besides the fact that there cannot be molecules outside a periodic box, are you sure that you want such a high SDS concentration? You are nearly 15 times over the cmc, in the real world you would most likely end up with a hydrated SDS crystals (Mol. Cryst. Liq. Cryst., Vol. 549:pp. 160–165, 2011)
On Thu, Jan 18, 2018 at 10:39 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/18/18 7:28 AM, za...@tezu.ernet.in wrote: > >> Dear Gromacs Users >> >> I am trying to simulate a protein with 200 SDS molecules. >> >> After inserting 200 molecules inside the box with the protein at the >> center (size of the cubic box is 324 nm3), few of the SDS molecules are >> outside the box from each side of the box. >> >> I have used the following command to insert the sds molecules: >> >> gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro >> >> Will it be appropriate to run simulation with this initial setup? Or do I >> need to make sure that entire sds molecules are inside the box. >> > > There is no such thing as "outside" a periodic box. > > -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. > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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.