A visualisation to help see what is going on with the PBC and the molecules https://twitter.com/dr_dbw/status/909559339366572032 Catch ya,
Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On 19 January 2018 at 01:03, André Farias de Moura <mo...@ufscar.br> wrote: > 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. -- 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.
