Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks
On Saturday, October 12, 2013 1:12 AM, Mass <masstransfer_2...@yahoo.com> wrote: Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul <jalem...@vt.edu> wrote: On 10/11/13 1:34 AM, Mass wrote: > Dear Mark, > Thanks for your comments, I uninstalled my previous Gromacs version ( from > Ubuntu software centre I just removed it) . and followed the dirty and quick > installation on Gromacs website > > tar xfz gromacs-4.6.3.tar.gz > cd gromacs-4.6.3 > mkdir build > cd build > cmake .. -DGMX_BUILD_OWN_FFTW=ON > make > sudo make install > source /usr/local/gromacs/bin/GMXRC > I have one question here, why when I run mdrun in my home directory it is > telling me that Gromacs is not installed, but when I source it again and go > to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time > Configure your login scripts to do it for you. > secondly when I do do_dssp > > do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc > Secondary_Structure_analysis_original_dss.xvg -ssdump > > > > I am getting following error > > Program mdrun, VERSION 4.6.3 > Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 > > Can not open file: > topol.tpr > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
