I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an alkyl chain hanging off a ring, and previous simulations have found ordering of the IL at the liquid-liquid surface as the molecules essentially lay themselves flat against the interface. I though Sz might illustrate that. The interface is perpendicular to the z vector.
I tried a few different commands. The latest was: g_order_mpi -f mdDone.trr -s md.tpr -n ndx-order.ndx -sl 50 -o order.xvg I can't figure out how to input the boolean for -szonly. I've tried "yes" "true" and "1" and it always tells me that's an "invalid command line argument." On Thu, Sep 10, 2015 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/10/15 1:58 PM, Stella Nickerson wrote: > >> I have a molecule with a carbon chain attached to a ring. I want to use >> g_order to generate the ordering parameter across the simulation box. I've >> read the manual entry for g_order, and it said to create an index file >> with >> only the "relevant" atoms included, so I made a group with just the atoms >> in the carbon chain and put it in an index file on its own with no other >> groups. >> >> The output file doesn't have any profile in it. It says the x axis is >> "Atom" which I don't want--I want the x axis to be "z" and the y axis to >> be >> "Sz." >> >> I've been playing with the arguments but nothing I try seems to make a >> difference. >> >> What am I doing wrong? >> >> > Without seeing your command(s), hard to say, but in principle you should > be able to get this with some combination of -sl -szonly, etc. Normal > usage of g_order is for alkyl chains of membranes, to calculate deuterium > order parameters. I'm not clear if that's what you actually want. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
