Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue. Google knows a lot more about it than anybody here ;-)
Mark On Fri, Oct 11, 2013 at 2:57 PM, Mass <masstransfer_2...@yahoo.com> wrote: > 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 > -- 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