Thanks you for directing me to the paper. Before I switch to off-line questions, do you recall what his inputs needed to be? I keep getting the error:
" Program: gmx densorder, version 2016.3 Source file: src/gromacs/gmxana/gmx_densorder.cpp (line 808) Fatal error: No or not correct number (2) of output-file-series: 1 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors " When I add the flag -Spect or -or after it finishes reading my trr file. Thank you, Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of David van der Spoel <sp...@xray.bmc.uu.se> Sent: Friday, August 31, 2018 5:46 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Documentation on gmx densorder? Den 2018-08-30 kl. 15:34, skrev Smith, Micholas D.: > Dear GMX users, > > > I was wondering if anyone has used the gmx densorder (originally g_densorder) > in the past utility in the past. I have system with an interface and the idea > of " > > gmx densorder reduces a two-phase density distribution along an axis, computed > over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a > functional profile for interfacial densities" seems rather interesting. > However, I haven't found any more documentation on this tool (i.e. what the > binary format of its output is actually used for). > > > If anyone has used it and has some pointers on what the output should be read > with, or remembers the paper(s) it originated from it would be quite useful. Guilty as charged: https://pubs.acs.org/doi/abs/10.1021/ct500459x It was the student who implemented the code and used it however, but feel free to contact me off line if you have more questions. > > > Thanks, > > > Micholas > > > =================== > Micholas Dean Smith, PhD. MRSC > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
